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16 March 2018, Volume 51 Issue 6

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CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS

Utilizing Probability Estimation Improves the Accuracy of Plant Variety Identification by Molecular Markers

ZHOU JunFei, CUI YeHan, TANG Hao, LI Lun, CHEN Hong, WEN Wen, HAN RuiXi, HUANG SiSi, FANG ZhiWei, PENG Hai

Scientia Agricultura Sinica. 2018, 51(6):  1013-1019.  doi:10.3864/j.issn.0578-1752.2018.06.001

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【Objective】 The current standards for plant variety identification only examine a small number of markers on the genome, which may lead to sampling errors, therefore identification conclusions are often questionable. The goal of this study is to estimate the sampling errors in plant variety identification procedure and evaluate the reliability of the conclusions, and eventually provide the scientific basis for the applications of molecular identification standards. 【Method】 Based on the number of observed differential loci between two varieties, a conditional probability model was established based on the Bayes’ theorem to estimate the true number of the different loci. Given that the observed number of differential loci between two varieties follows the binomial distribution, and the prior distribution of true number is an approximate uniform distribution, the conditional probability model was finally computed. Based on the confidence levels provided by the probabilistic model, the relationship between plant varieties is divided into the red, green or yellow zones, corresponding to the same or similar, different and undetermined varieties, respectively. To validate this probabilistic model, the genotyping data of 3 205 SSR molecular markers for each of the 8 rice varieties were used. For each pair of varieties, 10 000 sets of molecular markers were simulated, and each set is composed of 48 random SSR markers. For each simulation, the relationship between the varieties was estimated based on the probability computed by the model. And then the estimated relationship was compared with the real one to evaluate the accuracy of the probabilistic model. Finally, the probabilistic model was applied to provide probabilistic support for the conclusion of a recent watermelon variety infringement case. 【Result】The validation results showed that each pair of varieties was determined as different varieties in 4 295-10 000 simulations at a confidence level of 95%. Compared with the true relationship between varieties, the probabilistic model had an accuracy of 100% in determination of rice variety relationships. Finally, the court decision about the infringement dispute of watermelon varieties also was supported by the probabilistic model at a confidence level of 95%, indicating that the losing party's doubt on the limited number of the sampling loci is not sufficient. 【Conclusion】In this study, a probabilistic model was built to evaluation the reliability of the conclusion of the variety relationships, which provides confidence levels for the molecular identification conclusion of the relationship among varieties, and thus improves the accuracy, and finally avoids the controversies caused by the insufficient number of testing markers.

Genome-Wide Association Analysis of Silique Density on Racemes and Its Component Traits in Brassica napus L.

REN YiYing, CUI Cui, WANG Qian, TANG ZhangLin, XU XinFu, LIN Na, YIN JiaMing, LI JiaNa, ZHOU QingYuan

Scientia Agricultura Sinica. 2018, 51(6):  1020-1033.  doi:10.3864/j.issn.0578-1752.2018.06.002

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【Objective】 High yield of rapeseed (Brassica napus) has been regarded as one of the main research goals for breeders. Silique density, the number of valid siliques on racemes as well as them related traits, which are the main character to test yield level of rapeseed, have significant or extremely significant positive correlation with the yield. These results are helpful to further elucidate the genetic and molecular mechanisms of the siliques density and related traits of rapeseed. 【Method】 In this study, a natural populations contained 213 rapeseed cultivars (lines) with different genetic backgrounds were used to study genotyping via the Brassica 60 K Illumina Infinium SNP array. Valid length on racemes and valid silique on racemes were investigated at the fruit ripening stage in 2015 and 2016, respectively, at same time silique density on racemes was calculated. Furthermore, relative kinship and linkage disequilibrium of chromosome were analyzed by Tassel 5.1.0 software, and the population structure was analyzed using Structure 2.3.4 software. Then, based on the optimal model, important candidate genes related to traits were predicted by the genome-wide correlation analysis (GWAS) of the silique density on racemes and its component traits were conducted, according to the sequence of LD regions of the associated SNP array. 【Result】Population structure analysis showed that 213 varieties were divided into P1 and P2 subgroups, in which the P1 contained 50 varieties of rapeseed (23.5%) and the P2 contained 163 varieties of rapeseed (76.5%), and it was consistent with the geo-cultivation of rapeseed. Meanwhile, the results of phylogenetic relationship indicated that about 89.74% materials had kinship value less than 0.2, of which about 59.91% materials had almost little genetic kinship. Thus, it can be concluded that there was a relatively distant kinship among materials in this natural group. In addition, a linkage disequilibrium analysis of A and C genomes revealed that r2 of A and C genomes decreased with increasing genetic distance, and the attenuation distance of A genome is smaller than that of C genome. Based on the two-year data analyzed by GWAS, 17 SNP were detected to be significant correlation with the siliques density on racemes and its component traits. Among them, 7 and 9 SNPs associated with silique density and valid length on racemes, each of them explained 11.343%-15.96% and 9.67%-13.097% of phenotypic variation, respectively. And 1 SNP site was related to valid silique on racemes, explaining the phenotypic variation of 11.56%. 22 candidate genes associated with silique density on racemes and its component traits were found via the LD interval of the significant SNPs and corresponding interval sequences of Brassica napus. Specifically, some genes including BnaA01g16940D, BnaC01g38800D and so on controlled silique density on racemes and its component traits by regulating the synthesis and signal transduction of endogenous hormones such as GA and IAA. And some genes, such as BnaA01g16970D, BnaA03g29180D and so on, were related to regulate meristems development of floral while other genes, BnaC09g18690D and BnaC09g09210D were involved in division and cell growth of floral. 【Conclusion】 In this study, 17 SNPs were detected associated with the siliques density on racemes, the valid length on racemes and the valid silique on racemes. Furthermore, 22 candidate genes related to the siliques density on racemes and its component traits were screened out.

TILLAGE & CULTIVATION·PHYSIOLOGY & BIOCHEMISTRY·AGRICULTURE INFORMATION TECHNOLOGY

Research on Maize Plant Type Parameter Extraction by Using Three Dimensional Digitizing Data

WEN WeiLiang, GUO XinYu, ZHAO ChunJiang, XIAO BoXiang, WANG YongJian

Scientia Agricultura Sinica. 2018, 51(6):  1034-1044.  doi:10.3864/j.issn.0578-1752.2018.06.003

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【Objective】Morphological parameters acquisition of maize plant is an important part for maize breeding research. Now, the mainly acquisition method of plant type parameter is manual measurement, which has the problems of non-uniform standard, low accuracy and difficult to visualize, etc. Plant type parameter extraction from image or three dimensional (3D) point cloud depends on the algorithms of skeleton extraction, and it has a low accuracy of recent methods.【Method】In this paper, we proposed a maize plant type parameter extraction method by using 3D digitizing data. The maize plant skeleton data was obtained by using 3D digitizer, and an acquisition standard for maize stalk, leaf, tassel and ear was proposed to promise uniform morphological data. The 3D digitized data was regularized by moving to the origin of the space coordinate system and rotating parallel to the Z axis. Morphological parameters, including plant height, leaf insertion height, blade peak height, leaf length, leaf width, blade span length, leaf insertion inclination, and leaf azimuthal angle, were extracted according to the relationship of 3D digitizing point and the definition of each parameter. Exact formulas were given of each morphological parameter. Meanwhile, a novel method for calculating plant azimuth plane was proposed by iteratively for solving an L1 optimization problem, which is described by the minimum sum of every azimuth angle to the azimuthal plane. The algorithm could calculate the exact plant azimuthal range when the leaf number was even. An index called dev value was introduced to evaluate the deviation of maize leaves from the azimuthal plane. 【Result】 3D digital data and manual measured parameters of 6 different cultivars of maize plant, with the abbreviations of JK665, JK968, MC812, ND108, XY335 and ZD958, were obtained to verify the extraction method. Experimental results showed that the error of leaf length, leaf insertion inclination and leaf azimuth were very small, the corresponding RMSE (root mean square error) were 3.44 cm, 3.41°, and 8.23°, respectively. The MAPE (mean absolute percent error) of leaf length and leaf insertion inclination were 4.06% and 4.72%, respectively. The error of leaf width with RMSE = 0.8 cm and MAPE = 7.21%, was a little larger than other parameters, because the curve shape vertical to the midrib on the leaf was different. The novel azimuthal plane estimation method gave a quantitative description and derived better results than the averaged azimuth angle approach. The dev value could be used for estimating the spatial expansion of maize plants. In theory, larger dev value cultivar maize plants could intercept more photosynthetically active radiation. 【Conclusion】 The research provided an accurate, convenient and visual way for extracting and analyzing maize plant type parameters and had an important role in the optimization of maize plant type, functional-structural plant modeling, and plant phenotyping research.

Effects of Nitrogen Fertilizer on Dry Matter Accumulation, Transportation and Nitrogen Metabolism in Functional Leaves of Broomcorn Millet at Late Growth Stage

GONG XiangWei, HAN HaoKun, ZHANG DaZhong, LI Jing, WANG Meng, XUE ZhiHe, YANG Pu, GAO XiaoLi, FENG BaiLi

Scientia Agricultura Sinica. 2018, 51(6):  1045-1056.  doi:10.3864/j.issn.0578-1752.2018.06.004

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【Objective】 The propose of this study was to investigate the basis of nutritional requirement and supply on high quality of broomcorn millet through studying structure characteristics of dry matter and regularity of nitrogen metabolism in functional leaves of broomcorn millet at late growth stage under different nitrogen levels.【Method】Broomcorn millet cultivar of Yumi2 was selected as the material in a field experiment from 2015 to 2016. Dry matter accumulation, distribution and transportation were conducted at heading stage, flowering stage, filling stage and maturity stage under different nitrogen levels of 60 kg·hm^-2 (N1), 105 kg·hm^-2 (N2), 150 kg·hm^-2 (N3), 195 kg·hm^-2 (N4), and glutamine synthetase (GS) activity, nitrate reductase (NR) activity, free amino acids and soluble protein content in functional leaves were detected, as well as yield and yield components were analyzed. The correlation between the dry matter accumulation, transportation of broomcorn millet and nitrogen metabolism of the leaves or yield were summarized.【Result】The results showed that the accumulation of dry matter of above-ground organs increased with increasing N application rates up to 150 kg·hm-2, and then decreased when N application rate was 195 kg·hm^-2. The stem dry weight, leaves dry weight, sheath dry weight and spike dry weight under N3 treatment increased 51.2%, 40.8%, 64.2% and 41.3%, respectively, compared with the non-fertilization treatment at the flowering stage. Transportations of dry matters in different organs were improved by applying nitrogen fertilizer. Distribution rate of aboveground organs were increased to grain after heading, which increased 9.6% under N3 treatment, compared with the non-fertilization treatment. The GS activity, NR activity, free amino acid and soluble protein content in different leaves were upward-declined under nitrogen treatment. Nitrogen metabolism activities were the flag leaves > the second leaves >the third leaves at the same period, among them, N3 treatment reached the maximum value, but the overall change of nitrogen metabolism was not affected in functional leaves. Compared with no nitrogen application, the nitrogen content of grain under N1, N2, N3 and N4 treatments increased by 4.0%, 6.0%, 7.8% and 8.9%, respectively, and the protein content of grain by nitrogen fertilizers were significantly increased by 3.89%, 5.75%, 7.54% and 8.59%, respectively. The length of millet, the number of stalks, the number of panicles and the grain weight and the yield were also significantly increased by nitrogen fertilizer. Compared with no nitrogen application, in 2015, yield of broomcorn millet under N1, N2, N3 and N4 treatments were significantly increased by 10.09%, 29.71%, 44.73% and 35.99%, respectively. In 2016, which were significantly increased by 19.08%, 30.60%, 65.85% and 39.14%, respectively. The biggest increase in virginity was N3 treatment in two years. Therefore, N3 treatment was the best effect on increasing yield. 【Conclusion】The dry matter accumulation, transportation and nitrogen metabolism in functional leaves of broomcorn millet could be promoted by nitrogen fertilizer at late growth stage, and yield and yield components could be improved. Under this experimental condition, N3 treatment (150 kg·hm^-2) was the suitable amount of nitrogen in Yulin, Shaanxi.

The Evaluation of Chlorophyll Content Detection in the Leaves of Newhall Navel Orange Based on Different Sensors

LI WenTao, YANG JiangBo, ZHANG Ji, WANG KeJian, DENG Lie, Lü Qiang, HE ShaoLan, XIE RangJin, ZHENG YongQiang, MA YanYan, YI ShiLai

Scientia Agricultura Sinica. 2018, 51(6):  1057-1066.  doi:10.3864/j.issn.0578-1752.2018.06.005

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【Objective】 The objective of the study was to investigate the detection accuracy of chlorophyll content in the leaves of Newhall Navel Orange (Citrus sinensis Osbeck) based on different sensors with different scales and prediction models, so as to provide evidence for establishing an easy and high efficient nutrition diagnosis technology in citrus orchard.【Method】The spring shoot leaves of Newhall Navel Orange trees on trifoliate orange (Poncirus trifoliata (L.) Raf.) root stocks were selected for the study. Using the FieldSpec4, Multiplex®Research, digital image technology and SPAD-502 chlorophyll meter to obtain the leaf spectral, fluorescent values, digital indicators and chlorophyll content (SPAD values). In addition, the association of leaf spectral, fluorescent values and digital indicators with chlorophyll content were analyzed. The chlorophyll content quantitative inversion model was established by means of univariate and multiple regression (partial least square regression, PLS). Then the model accuracy and feasibility of the monitoring of leaf chlorophyll content based on different sensors were evaluated. 【Result】The results showed that the correlation between the content of relative chlorophyll content and parameter information from FieldSpec4, Multiplex®Research, digital image technology were extremely significant, and their relative coefficients were all more than 0.7. The goodness-of-fit of the predictive models were good. Among them, the PLS models based on FieldSpec4 established by First-order derivative (FD) method at the band of 532 nm, 586 nm and 705 nm showed the best goodness-of-fit with MRE (mean relative error) =1.80%，RPD (residual prediction deviation) =3.801. The quadratic regression model based on digital image technology which chose G-B values as characteristic indicators was established with MRE=1.98%, RPD=3.946. The PLS models was established by using the characteristic fluorescent parameters based on Multiplex®Research with MRE=2.37%, RPD=4.807.【Conclusion】The results showed that it had a certain feasibility by using information obtained from FieldSpec4, Multiplex® Research, digital image technology to predict chlorophyll content of citrus single leaves. The prediction accuracy of FieldSpec4 was best, the Multiplex ® Research was most convenient, and the digital image technology was more suitable for detection of large quantities of samples.

PLANT PROTECTION

Induced Immunity Effect and Mechanism of the Weak Pathogenicity Isolate of Verticillium dahliae Vd171 Against Verticillium Wilt in Cotton

ZHANG YiHao, FENG HongJie, YUAN Yuan, JIN YuYing, SHI YongQiang, ZHANG ChaoJun, LI FuGuang

Scientia Agricultura Sinica. 2018, 51(6):  1067-1078.  doi:10.3864/j.issn.0578-1752.2018.06.006

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【Objective】 The objective of this study is to clarify the induced immunity effect and mechanism of the weak pathogenicity isolate of Verticillium dahliae Vd171 against Verticillium wilt in cotton, and to provide a basis for exploring new ways of biological control of Verticillium wilt in cotton. 【Method】 The weak pathogenicity isolate of V. dahlia Vd171 was used to evaluate the induced immune effects of different inoculation methods, inoculation periods, inoculation times and inoculum types in greenhouse. Different inoculation methods included root-dipping, root-irrigation, stem-injection, foliar-spraying and seed-soaking by Vd171 spore suspension with 1×10⁷ conidia/mL. Ten mL spore suspension for each pot was used in root-dipping, root-irrigation and foliar-spraying and 0.2 mL for each plant in stem-injection. The seeds were soaked for 12 h with spore suspension. Seven treatments were set to confirm the inoculation periods of Vd171 which including 2, 4, 6, 8 days before inoculated Vd080 (a high pathogenicity isolate of V. dahliae) and 1, 2, 4 days after inoculated Vd080. The inoculation times of Vd171 was one or two times before inoculated Vd080. The inoculum types included spore suspension and filtrate of Czapek of Vd171. The cotton seedlings were cultivated by hydroponics and inoculated by Vd080_GFP 4 days after Vd171. Then the roots were collected in different times and the spores of Vd080_GFP were washed in sterile water. The colonization of Vd080_GFP on cotton rootwas analyzed by counting the spores of Vd080_GFP under microscope. Furthermore, in order to analyze the extension of Vd080 in cotton stem, the small hypocotyl pieces was cultivated on PDA plates at the 7th day after inoculated by Vd080_GFP. The transcript level of 4CL, CHI, POD, PPO and PAL was analyzed by qPCR. The enzyme activity of POD, PPO, PAL and CHI was measured. The sedimentation of lignin was observed by phloroglucinol staining and the reactive oxygen species (ROS) of leaves was observed by DAB staining. 【Result】 The highest control efficacy was obtained when Vd171 was inoculated 4 days prior to inoculation by Vd080 (control efficacy of 89.4%). The control efficacy had significant differences among the five inoculation methods. Root-dipping treatment provided a control efficacy of 70.0%, followed by foliar-spraying (54.3%), seed-soaking (45.0%), root-irrigation (39.0%), and stem-injection (2.2%). There was no statistical significant difference between the control efficacy against Vd080 of pre-inoculated by Vd171 for one and two times (85.6% and 81.4%). Particularly, both cotton pre-inoculated with conidiospore and culture filtrate of Vd171 treatments could reduce disease indices of Verticillium wilt, with the control efficacy of 85.6% and 81.1%. There was no significant difference between the two treatments. Cotton plants pre-inoculated with Vd171 could reduce the colonization of Vd080 in cotton root and prevent its expansion in cotton stem. In addition, the transcript level of GhPAL, Gh4CL and GhCHI increased significantly by induction of Vd171, which was 2.2, 8.5 and 2.6 times of the control treatment, respectively. The activity of PPO, PAL, POD and CHI in hypocotyl increased by 31.9%, 131.0%, 57.1% and 102.1% than that of control treatment, respectively, and activity of PAL, CHI and POD in cotyledon also remarkably increased by 22.1%, 39.6% and 7.1% than that of control treatment, respectively. Meanwhile, sedimentation of lignin and ROS were induced by Vd171.【Conclusion】 The weak virulent isolate Vd171 can effectively induce cotton resistant to Verticillium wilt and has a good application prospect in the control of Verticillium wilt in cotton.

Identification and Analysis of Magnaporthe oryzae of Foxtail Millet Avirulence Genes

REN ShiLong, BAI Hui, WANG yongFang, QUAN JianZhang, DONG ZhiPing, LI ZhiYong, XING JiHong

Scientia Agricultura Sinica. 2018, 51(6):  1079-1088.  doi:10.3864/j.issn.0578-1752.2018.06.007

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【Objective】The objective of this study is to identify avirulence genes (Avr-genes) of Magnaporthe oryzae, understand the distribution and variation of Avr-genes in the epidemic strains of different regions, and to provide a reference for further study of the mechanism of Avr-genes variation in M. oryzae. 【Method】 A total of 76 strains of M. oryzae were isolated from different regions of millet growing area in northern China. The genomic DNA of 76 M. oryzae strains was extracted and used as a template for PCR amplification using the specific primers designed according to the 7 Avr-genes cloned from rice blast. AGE (agarose gel electrophoresis) analysis and sequencing of the PCR products were used to analyze the distribution of Avr-genes in M. oryzae strains of different regions from foxtail millet. 【Result】 The amplification rate of ACE1, Avr-pita, Avr1-CO39 and AvrPiz-t genes was 100% in 76 strains of M. oryzae and the amplification rate of avirulent genes Avr-pik, Avr-pia and Avr-pii was 63.2%, 42.1% and 21.1%, respectively. The amplification of Avr1-CO39 in the strains P11 and P34 was about 490 bp larger than the expected fragments. Sequencing of the Avr1-CO39 in the strains P11 and P34 showed that the Avr1-CO39 sequences in strains P11 and P34 were identical and the promoter region contained a 490 bp inserted fragment which shared 99.16% similarity with non-LTR retrotransposon: Mg-SINE. A high level of Avr-pita polymorphisms were found in M. oryzae and the major variation was single nucleotide variation, including single base insertion, deletion, and SNP of multiple loci. The main sequence variation of Avr-pia was the absence of the whole Avr-gene, and their sequencing verification results showed that there were 4 genotypes of Avr-pia allele in the strains. The Avr-pia-A was identical to the reference sequence (AB498873.1) and contained 10 strains. Avr-pia-B contained 20 strains, and there were C/T, G/T and C/A mutations at -116, -109, and -16 bp sites, but the CDS region of Avr-pia-B was the same as the reference sequence. The Avr-pia-C type contained only the strain P10, and there was a T/G mutation at +150 bp, but it is a synonymous mutation. The Avr-pia-D contained only the strain P18, and there was a C/T mutation at +212 bp site, which resulted in the mutation of coding amino acid from threonine to isoleucine. The Avr-pii of M. oryzae contained 3 alleles. The Avr-pii-A was the same as the reference sequence (AB498874.1) and contained 14 strains. An A/G mutation was found in Avr-pii-B and Avr-pii-C at +139 and +64 bp sites, respectively, which caused the amino sequence in the site to mutate from threonine to alanine. Avr-pii-B and Avr-pii-C were both reported for the first time. The haplotype analysis showed that AG2 containing 23 strains was the dominant type, which accounted for 30.2% of the tested strains. 【Conclusion】 Avr-genes ACE1, Avr-pita, Avr1-CO39 and AvrPiz-t had no geographical origin difference and the frequency distribution of Avr-genes Avr-pik, Avr-pia and Avr-pii varied in different regions. The AG2 haplotype was predominant in M. oryzae from foxtail millet, followed by AG1 and AG5 haplotypes.

SOIL & FERTILIZER·WATER-SAVING IRRIGATION·AGROECOLOGY & ENVIRONMENT

Framing the Spatio-Temporal Changes in Global Cultivated Land Using GlobeLand30

CHEN Jun

Scientia Agricultura Sinica. 2018, 51(6):  1089-1090.  doi:10.3864/j.issn.0578-1752.2018.06.008

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Spatio-Temporal Changes in Global Cultivated Land over 2000-2010

HU Qiong, WU WenBin, XIANG MingTao, CHEN Di, LONG YuQiao, SONG Qian, LIU YiZhu, LU Miao, YU QiangYi

Scientia Agricultura Sinica. 2018, 51(6):  1091-1105.  doi:10.3864/j.issn.0578-1752.2018.06.009

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【Objective】This study is to analyze the spatial distribution and spatio-temporal change patterns of global cultivated land so as to provide important insights for national food security decision-making and global ecological environment monitoring. 【Method】To do so, this study analyzed the spatial distribution of global cultivated land in 2010, spatio-temporal change patterns of global cultivated land area and land use intensification during 2000-2010 by using eight statistical indicators, i.e., cultivated land area, changed area, standard deviation of changed area, percentage change of area, cultivated land area per capita, multiple cropping index, change and percentage change of multiple cropping index at three statistical scales, i.e., continent, country and 1°×1° grid. 【Result】The analysis results show the global total cultivated land area is 193 890.00×10⁴ hm² , which accounts for 14.31% of global total land area. The global average cultivated area per capital is 0.28 hm² in 2010, among which Oceania ranks first (1.71 hm²) and Asia comes last (0.17 hm²). Regions in [10^oN-45^oN, 65^oE-125^oE], [40^oN-55^oN, 15^oE-55^oE] and [15^oS-45^oS, 45^oW-70^oW] have the largest cultivated land area over the world. The top ten countries with largest cultivated land area are: China, the United States, India, Russia, Brazil, Argentina, Australia, Canada, Kazakhstan and Ukraine, among which Russia, Canada, Argentina and Australia are also among the top ten countries in cultivated area per capita. During 2000-2010, global cultivated land has a slight increase of 2.19%, among which America has the largest increase in cultivated land area, with a increase of 2 128.14×10⁴ hm², and Africa has the biggest increase rate and spatial variation of cultivated land area, with increase percentage of 7.42%. Among the global top ten countries with the largest cultivated land area, China is the only country where cultivated land area declined during 2000-2010, with the decrease percentage of 0.95%, and Brazil and Argentina changed most both in total cultivated land area and spatial area distribution, and the United States has the least change both in total area and percentage change of area. Regions with the highest agricultural cropping intensity concentrated in South-east Asia, Central America and West Africa, all of which have multiple cropping index of more than 200%. Five countries of the top ten with the largest cultivated land area show increase in multiple cropping index from 2000 to 2010, among which Brazil and Kazakhstan increased most and Russia decreased most. 【Conclusion】Global cultivated land generally keeps stable during this period, but there is obvious difference across regions and nations. Our study analyzed the current status of global cultivated land distribution and its change during 2000-2010 based on the 30 meter global land cover data. The results in this study provide important information and data for studies of global water resources use, global production change and food security in the future.

Changes of Cultivated Land Utilization Pattern in Asia from 2000 to 2010

CHEN Di, WU WenBin, ZHOU QingBo, HU Qiong, XIANG MingTao, LU Miao, YU QiangYi

Scientia Agricultura Sinica. 2018, 51(6):  1106-1120.  doi:10.3864/j.issn.0578-1752.2018.06.010

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【Objective】Asia has the largest population, the biggest cultivated land quantity, and a lot of developing countries. The change characteristics of Asian cultivated land utilization are related to national and global grain production fluctuation, and impact on world food security. By analyzing Asian cultivated land utilization pattern change, the understanding of Asian cultivated land utilization pattern was deepened, the change characteristics and laws were mastered scientifically. It provides the basis for Asian agricultural land system research.【Method】Based on the FAOSTAT statistics data and the latest China's 30 meter resolution global land cover data product (GlobeLand30) in 2000 and 2010, two indicator groups were built to analyze the change characteristics of cultivated land utilization pattern in Asia during 2000-2010, including cultivated land quantity indicator group and cultivated land use pattern indicator group. Six indicators which selected from two indicator groups were calculated, including cultivated land area, multiple cropping index and fragmentation index in 2010 and their change percentage during ten years. The change characteristics of cultivated land quantity, multiple cropping index and fragmentation index from 2000 to 2010 were discussed from three scales, including the country level, geographical zones and the county level. 【Result】 Results showed: the cultivated land area of Asia was 69 827.94×10⁴ hm² in 2010; during the past ten years, the cultivated land loss was 62.62×10⁴ hm², and area of Asian cultivated land generally increased by 0.09% with decrease of cultivated land in East Asia and increase of other regions of Asia. The growth rate of Southeast Asia was biggest and West Asia was the most active area of cultivated land increase and decrease. In Asia, 60% of the countries' cultivated land has increased, and 80% of the countries' cultivated land has changed from -5.00% to 5.00%. From 2000 to 2010, the multiple cropping index increased 7.77% in Asia, and the change percentage was 9.00%. It also increased in every geographical zones of Asia. More than two-thirds of the countries' multiple cropping index has increased, but western Asia's Saudi Arabia, Qatar, Cyprus and other countries have seen a significant reduction. The areas of Asian fragmented cultivated land were mostly concentrated in southern China, Japan, the Philippines and Afghanistan, while India, North China Plain and the Northeast agricultural reclamation area have large parcels. The change percentage of fragmentation index in Asia was 1.12% with increased acutely in Southeast Asia but declined dramatically in Central Asia and South Asia. Over half of countries in Asia had the decreased fragmentation index. In China, during the past decade, cultivated land quantity declined 0.95%, multiple cropping index increased 6.01%, and fragmentation index increased 2.17%. The south region had the high fragmentation index, but main grain production regions, such as North China plain, the northeast land reclamation district and Chengdu plain, had the low fragmentation index. The fragmentation index of economically developed areas in the east and north China increased, but decreased in Hunan and Jiangxi Province. 【Conclusion】 Generally speaking, the change of Asian cultivated land quantity was relatively steady, and the area increased slightly. The multiple cropping index showed high in the south and low in the north. It was a remarkable fact that the growth rate in Southeast Asia was higher than other regions, and the multiple cropping index reduced in northwest of Asia. It was indicated that the cultivated land utilization ratio in Asia had a great improvement. The fragmentation index of Asia increased little in the past decade. Over half of the countries’ cultivated land had the large-scale development. As the key agricultural district of Asia, the cultivated land of China reduced slightly and became more broken, but the cultivated land utilization has increased substantially.

Spatial-Temporal Changes in Cultivated Lands in Europe over 2000-2010

XIANG MingTao, WU WenBin, HU Qiong, CHEN Di, LU Miao, YU QiangYi

Scientia Agricultura Sinica. 2018, 51(6):  1121-1133.  doi:10.3864/j.issn.0578-1752.2018.06.011

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【Objective】Aimed at exploring quantity, range, spatial position and conversion types of cultivated land change in Europe over 2000-2010, the study scientifically described general characteristics of cultivated lands in Europe during the ten years. 【Method】Based on GlobeLand30, mathematical statistics method, spatial analysis of GIS and batch processing of Python were applied to compute multi-dimensional indicators, such as quantity, range, variance of cultivated land change, cultivation index, as well as conversion-in rate and conversion-out rate of cultivated land area. 【Result】The total cultivated land area of Europe in 2010 was 42820.84×10⁴ hm². Different region had different proportions: east Europe (51.17%), south Europe (19.07%), central Europe (13.62%), west Europe (13.31%), and north Europe (2.83%). The distribution of cultivated land in Europe was relatively concentrated. The European cultivated land Top 10 countries composed 82.17% of European total cultivated land in 2010. Generally the cultivated land area increased 220.90×10⁴ hm² over 2000-2010 in Europe and the percentage was only 0.52%. To be specific, the foot of mountains and the sides of rivers were the expansion areas, but cultivated lands in the high altitudes and cold climate. The cultivated lands in north Europe (1.25%), east Europe (0.88%) and west Europe (0.64%) increased in different degrees, while the rest decreased. In north and east Europe, the change of cultivated land area was drastic within a country, while it was opposite in west and central Europe. In south Europe, the change of cultivated land area varied from country to country. The total cultivation index of Europe in 2010 was 18.71%. And five geographical zones ranked from high to low were: west Europe (61.17%), central Europe (57.64%), south Europe (49.24%), east Europe (12.20%), and north Europe (9.16%). Furthermore, the conversion between cultivated lands and other lands cover types only accounted for 4%, among which the conversion between cultivated land and forest, grassland, shrubland, artificial surfaces were the most obvious. In east Europe, vast grassland conversed most to cultivated land, while what conversed most to cultivated land in south Europe, west Europe and central Europe was artificial surface. 【Conclusion】Cultivated lands in Europe mainly concentrated in East Europe, while certain countries located in islands, mountainous areas and cold climate zones had few cultivated lands. At a spatial scale, cultivated lands in Europe appeared stable in the majority with some small change. Generally the change of cultivated land area was mild within a country but still had marked regional difference. During the ten years, the increases of cultivation index were slight. Although the proportion of conversion between cultivated land and other land cover was small, it still had predominantly regional difference. Tiny increase in forest and artificial surfaces but sharp reduction in grassland in contrast caused potential pressure to ecological environmental protection and sustainable development of cultivated lands. The findings could provide scientific support to the national agricultural trade, the “Agricultural Going-out”, utilities of domestic and foreign resources as well as the national strategy of propelling “The Belt and Road”.

Spatio-Temporal Changes in America’s Cropland over 2000-2010

LONG YuQiao, WU WenBin, HU Qiong, CHEN Di, XIANG MingTao, LU Miao, YU QiangYi

Scientia Agricultura Sinica. 2018, 51(6):  1134-1143.  doi:10.3864/j.issn.0578-1752.2018.06.012

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【Objective】The analysis of the spatial and temporal pattern of cropland is one of the hot issues of land surface research. As the world's most important grain production area, a spatio-temporal pattern analysis of America provides regional insight for cropland sustainable development with potential global applications.【Method】GlobeLand30—Cropland, mathematical statistics and GIS-based spatial analysis methods were adopted to explore the spatial-temporal characteristics of cropland area and conversion in America from 2000 to 2010, with particular emphasis on the Amazon region.【Result】This analysis shows that the total cropland area increased by 4.19% from 2000 to 2010 with 2 128.14×10⁴ hm², mainly converted from forest and grassland. The main conversion from cropland was to artificial surfaces. The major cropland expansion happened in Brazil with a rate of 9.51%, followed by Argentina. Ecuador showed the greatest decrease with 101.14×10⁴ hm². From 2000 to 2010, the multiple cropping index increased across the entire region by 2.42%, with Paraguay and Puerto Rico exhibiting the most significant changes. The United States of America had the most cropland area, however growth rate was only 0.08% and the multiple cropping index decreased by 0.89%. Brazil had the second highest amount of cropland area and a high rate of increase (9.51%), with most of the new cropland converted from forest and grassland. As the most important agricultural district and ecoregion in America, the Amazon experienced a cropland increase of 8.41%, with the direct conversions mostly occurring in the southwest of Brazil and Ecuador.【Conclusion】The total amount of cropland in America increased during 2000-2010, but there were large differences between countries. The direct conversions to cropland were mainly from woodlands, grasslands and shrubland in Brazil and Argentina. Loss of cropland was primarily caused by conversion to artificial land. Additionally, the Amazon experienced a steady increase in both the area of cropland and the multiple cropping index. While these increases bolster the regional and global grain production, the ecological environmental effects require more consideration.

Changes in Africa’s Cultivated Land Use and Its Eco-Environmental Factors Over 2000-2010

ZHANG Li, WU WenBin, SONG Qian, ZONG ZhaoWei, HU Qiong, XIANG MingTao, LU Miao

Scientia Agricultura Sinica. 2018, 51(6):  1144-1155.  doi:10.3864/j.issn.0578-1752.2018.06.013

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【Objective】 The objective of this study is to investigate the arable land resources of Africa, the second largest continent in the world, to accurately reveal the dynamic changes in cultivated land use and its eco-environmental factors over 2000-2010. 【Method】 The 2000 and 2010 Africa’s cultivated land layers of GlobeLand30, the world's first global land cover datasets at a 30 m resolution, were combined to understand the area, spatial pattern and intensive use changes in cultivated land at different scales and regions. 【Result】 During 2000-2010, the total cultivated land in Africa had increased by 1 540.06×10⁴ hm², with a net change rate of 7.42%. At regional level, Central Africa (10.42%) had the largest change rate of cultivated land use, which was followed by East Africa (9.49%), West Africa (7.55%), North Africa (6.74%) and South Africa (4.86%). The top ten countries with largest increase of cultivated land area were: Nigeria, Tanzania, Sudan, Kenya, Mozambique, Chad, Algeria, Zambia, Zimbabwe, and Burkina Faso, while Cote d’Ivoire, Mali, Angola, Ghana, Malawi, Tunisia, Burundi, Rwanda, Congo, and South Africa were the top ten countries with largest decreased cultivated land area. The multiple cropping index was 98.11% in 2010 and its change rate was 13.54% during 2000-2010. There was obvious difference in cultivated land change across regions. In general, cultivated land increased at longitude or latitude zones, among which the Eastern Hemisphere and Northern Hemisphere increased most. The increased cultivated land was mainly from forest, grassland and shrub, accounting for 15.19%, 66.37% and 11.20%, respectively, while the decreased cultivated is due to the conversion from cultivated land to forest, grassland and shrub, accounting for 21.15%, 61.19% and 11.78%, respectively. The area of increased cultivated land was much larger than the decreased cultivated land. In terms of the relationships between cultivated land change and eco-environment factors, the most obvious change in cultivated land were at zones with average temperature of 20-30 ºC and an average annual precipitation of 600-1 200 mm, and zones with elevation of 500-1 000 m and slope of less than 2 degrees. 【Conclusion】 The cultivated land area as well as its spatial patterns in Africa changed significantly over 2000-2010, and there were obvious differences across regions and countries. This study has explored the change characteristics of spatio-temporal patterns of cultivated land in Africa, the results of which provides the essential information for analyzing the spatial distribution of global cultivated land and understanding the change patterns and associated differences across different regions. It can also offer scientific guidance on agricultural decision making and land ownership adjustment in regions with significant cultivated land change so as to improve its food production and to guarantee the global food security.

Change in Cultivated Land Use Pattern in Oceania Based on GlobeLand30

CAO JunJun, WU WenBin, LIU YiZhu, HU Qiong, CHEN Di, XIANG MingTao, ZHOU QingBo

Scientia Agricultura Sinica. 2018, 51(6):  1156-1166.  doi:10.3864/j.issn.0578-1752.2018.06.014

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【Objective】The cultivated land change are more intense due to the latitudes of Oceania North and South have significant differences in climate and various types of food production in response to climate change is extremely sensitive. This paper analyzes the spatial and temporal changes of the cultivated land use pattern in Oceania, and scientifically grasps its characteristics and laws, which provides useful reference for the utilization of cultivated land and the development of grain policy.【Method】To do that, GlobeLand30, the two global 30 meters land cover remote sensing data product with 2000 and 2010 data, is newly constructed to establish three index sets, such as cultivated land quantity index, cultivated land use pattern index and cultivated land conversion index. The characteristics of cultivated land use in Oceania from 2000 to 2010 were analyzed from multiple angles: the national scale, 10 km×10 km grid scale and 30 m pixel scale.【Result】From the perspective of the change of cultivated land area, the cultivated area of Oceania increased by 3.79% from 2000 to 2010, and the largest increase in cultivated land area was Australia, with an increase of 5.39%. The largest additions of the area were mainly concentrated in the upper reaches of the Murray-Darling River Basin, east of the Oita Mountains in Australia. The area of reduced cultivated land was mainly in the northern islands of New Zealand, the east coast of Australia, and the eastern island of Papua New Guinea. The average per capita cultivated land in the major countries decreased by 21.47% and the largest decrease in farmland per capita was New Caledonia. From the perspective of the change of cultivated land use intensity, the average cropping index of major countries increased by 20.63%, and the average fragmentation of cultivated land decreased by 22.88%. The coordination degree of the cultivated area - compound index is more elastic. There are obvious differences in the driving mechanism of cultivated land fragmentation between Australia and New Zealand. In terms of the conversion characteristics of cultivated land types, Australia was the country with the largest change of cultivated land area in 2000 and 2010. In 2000, the change area transferred out of the total cultivated land was 630.25×10⁴ hm², and conversion to grassland accounted for 74.77% of all other outbound areas. In 2010, the total cultivated area transferred from the grassland was 544.95×10⁴ hm², accounting for 59.72% of the total transferred land area. In the whole continent, the conversion area between cultivated land and grassland was the largest, but the net increase in cultivated land was the largest contribution to the shrub land, a net increase of 165.03×10⁴ hm².【Conclusion】In general, the change of cultivated land area in Oceania is more intense, the intensity of cultivated land use is overall improved, the conversion of cultivated land and grassland is the most frequent.

HORTICULTURE

Progresses in Research on Molecular Biology of Abiotic Stress Responses in Vegetable Crops

GUO YangDong, ZHANG Lei, LI ShuangTao, CAO YunYun, QI ChuanDong, WANG JinFang

Scientia Agricultura Sinica. 2018, 51(6):  1167-1181.  doi:10.3864/j.issn.0578-1752.2018.06.015

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As an important economic crop, acreage, yield and demand of vegetable have been increased in recent years. Vegetables are inescapably affected by abiotic stresses including drought, salt, extreme temperature, heavy metal. These stresses seriously affect yield and quality of vegetable crops. During the recent decade, the studies on vegetables against abiotic stress have made some progress. Studies about drought stress focused on transcription factors such as DREB, WRKY, NAC, bHLH and bZIP in vegetables. These transcription factors were induced by drought stress and regulated the expressions of downstream genes to resist drought stress. Water transport genes (PIP, TIP), E3 ligase SIZ1 and DHN were also reported to be drought induced, and they rebalanced water potential, osmotic potential and reduced the ROS accumulation. The SOS pathway is critical in resisting salt stress. SlSOS2 upregulated the expressions of SlSOS1 and LeNHX2/4, which could maintain ion homeostasis and regulate the distribution of Na+ in plant organs under salt stress. To resist salt stress, NAC, ERF and MYB responded to salt stress and induced the expressions of tolerance-related genes. Furthermore, the synthesis of osmolyte is a common way to resist salt stress in vegetables. PvP5CS, tomPRO2 and BoiProDH improved the accumulation of proline, and SlBADH synthesized betaine under salt stress condition. As for extreme temperatures, extremes of cold and heat are threats to the plant growth. In response to high temperature stress, HSFs are the core of the regulatory network and can regulate series of anti-stress genes; including HSPs. SlHSFs formed a complex with each other to regulate the expressions of SlHSPs to resist heat stress in tomato. CBFs/EREBs were the core factors of cold stress and regulated by ICE1. LEA and HSPs prevented protein denaturation and maintained cell membrane fluidity at low temperature. To resist heavy metal stress, vegetables mainly depend on isolation in vivo and chelation mechanism in vivo and in vitro. In response to abiotic stresses in vegetables, ABA plays a crucial role as a signaling receptor. NAC, MYB, HSF and other transcription factors were induced by ABA signaling and responded to abiotic stress. These transcription factors enhanced the scavenging capacity of reactive oxygen species and synthesize more anti adversity substances in vegetables to resist multiple abiotic stresses.

Molecular Cloning and Functional Characterization of Purple Acid Phosphatase Related Gene MdPAP10 of Apple

LI Rui, AN JianPing, YOU ChunXiang, WANG XiaoFei, HAO YuJin

Scientia Agricultura Sinica. 2018, 51(6):  1182-1191.  doi:10.3864/j.issn.0578-1752.2018.06.016

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【Objective】This study is aiming at cloning apple purple acid phosphatase gene MdPAP10 and studying its expression pattern and low phosphorus response process. The mechanism of action of MdPAP10 under low phosphorus condition was further studied. This study laid the foundation for further study of the molecular mechanism of MdPAP10 affecting phosphorus uptake in woody fruit trees. 【Method】MdPAP10 gene was cloned by homology sequence alignment and PCR technique from Malus× domestica ‘Royal Gala’ apple.The protein structure of MdPAP10 was analyzed by NCBI and the PAP10 amino acid sequences of 10 species such as white pear, peach and strawberry were obtained. The phylogenetic tree was constructed by MEGA5.0. The induced expression and tissue-specific expression profiles of MdPAP10 gene in apple with low phosphorus stress were detected by real-time fluorescent quantitative PCR (qRT-PCR). MdPAP10 was ligated into the plant overexpression vector pBI121. The resultant construct was transformed into LBA4404 Agrobacterium, for the infection of apple calli. MdPAP10 transgenic calli were obtained by screening on resistant medium and PCR identification. The acid phosphatase accumulation and the tolerance to low phosphorus stress and phosphorus content were detected by culturing MdPAP10 transgenic calli on low phosphorus medium. Finally, qRT-PCR was used to detect the expression of phosphorus-related genes in MdPAP10 transgenic calli. 【Result】An apple purple acid phosphatase gene MdPAP10 (MDP0000272096) was cloned from Malus × domestica ‘Royal Gala’. Sequence analysis showed that the open reading frame (ORF) of MdPAP10 is 1 332 bp, which encoded 443 amino acids. Protein structure analysis showed that MdPAP10 contained a signal peptide and a phosphatase domain. Gene structure analysis showed that MdPAP10 contained 5 exons and 4 introns. A phylogenetic tree indicated that the apple MdPAP10 exhibited the highest sequence similarity to Pyrus bretschneideri PbPAP10. Expression analysis showed that MdPAP10 was expressed in roots, stems, leaves, flowers and fruits, and the expression level in roots was the highest. MdPAP10 had a significant response to low phosphorus conditions, and the expression level in roots increased gradually, reached the maximum at 6 h and then decreased gradually. The expression level in leaves was always lower than that in the control group. MdPAP10 transgenic calli were obtained by Agrobacterium tumefaciens infection and verified by PCR and qRT-PCR. MdPAP10 transgenic calli can significantly advance the secretion of acid phosphatase in low phosphorus conditions. Overexpression of MdPAP10 in transgenic calli under low phosphorus conditions improved the tolerance of calli to low phosphorus stress and increased the uptake of phosphorus. The result of qRT-PCR showed that overexpression of MdPAP10 could significantly promote the expression of apple phosphorus-related genes. 【Conclusion】MdPAP10 can respond significantly to low phosphorus stress and promote phosphorus uptake and acid phosphatase secretion under low phosphorus conditions. MdPAP10 plays an important regulatory role in response to low-phosphorus stress.

ANIMAL SCIENCE·VETERINARY SCIENCERE·SOURCE INSECT

An Electrochemical Aptasensor for Detection of Samonella typhimurium with Methylene Blue as Hybridization Indicator

XU LianYing, PENG HaiXia, SHAO YuYu, WANG BiNi, ZHANG FuXin

Scientia Agricultura Sinica. 2018, 51(6):  1192-1201.  doi:10.3864/j.issn.0578-1752.2018.06.017

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【Objective】A novel assay of electrochemical aptasensor for quantitative detection of Salmonella typhimurium with better practicability was constructed and investigated in order to overcome the shortcomings of traditional Salmonella detection methods, such as time-saving, sensitivity, simplicity, and etc.【Method】The prepared graphene oxide (GO) solution was dropped onto the glassy carbon electrode (GCE) surface and was reduced in PBS buffer by electrochemical reduction method to obtain reduced graphene oxide (rGO), and then Au nanoparticles (AuNPs) were electrochemically deposited onto the electrode by submersion in HAuCl_4. The complementary strands of the aptamers of Salmonella typhimurium (S) were attached to the surface of rGO/AuNPs GCE by Au-S bond, and then the electrode surface was blocked with MCH. Subsequently, the aptamers of Salmonella typhimurium (Apt) were dripped onto the modified electrode to make Apt bind with S. The modified electrode was immersed into the mixture containing Salmonella typhimurium and exonuclease I (Exo I) at 37 °C. In terms of the characteristics of Exo I that could amplify electrical signals and the aptamers that could exclusively bind with Salmonella typhimurium, the aptamers were taken away from S circularly. Then, the modified electrode was immersed in methylene blue (MB) solution for a while. Finally, the conditions of the incubation time in bacteria liquid, the Exo I concentration were optimized and the electrical signals of the electrode surface was monitored to construct the aptasensor. This electrochemical aptasensor was used to test Escherichia coli, Staphylococcus aureus, Shigella, Listeria monocytogenes and Vibrio parahaemolyticus to ensure the electrochemical aptasensor’s specificity. The electrochemical aptasensor was used to detect 2×10²-2×10⁷ cfu/mL Salmonella typhimurium to ensure the electrochemical aptasensor’s sensitivity. Then this electrochemical aptasensor was used to detect the pork to evaluate the practical use of electrochemical aptasensor.【Result】The optimization of the electrochemical aptasensor incubation time in bacterial liquid and the Exo I concentration were studied in detail, and the optimal conditions were 40 min and 0.8 U·μL^-1. The developed aptasensor was specific to Salmonella typhimurium and doesn’t react with non-target bacteria. The electrochemical aptasensor can successfully detect the Salmonella typhimurium target down to 67 cfu/mL. A good recovery of Salmonella typhimurium in the range of 97.3%-106.7% was obtained in pork by electrochemical aptasensor assays developed.【Conclusion】This electrochemical aptasensor can detect Salmonella typhimurium with a high sensitivity, a high specificity, an easy operation, a rapid detection and a low cost, which provide a good application prospect in the field of rapid quantitative detection of Salmonella typhimurium.

Comparison and Analysis of Genetic Parameters Estimation of Early Growth Traits of Alpine Merino Sheep by Different Animal Models

ZHANG JianBo, YUAN Chao, YUE YaoJing, GUO Jian, NIU ChunE, WANG XiJun, WANG LiJuan, Lü HuiQin, YANG BoHui

Scientia Agricultura Sinica. 2018, 51(6):  1202-1212.  doi:10.3864/j.issn.0578-1752.2018.06.018

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【Objective】This study aims to investigate the effect of different animal models on the estimation of genetic parameters of early growth traits of Alpine Merino Sheep, and to select the best animal model. And the best model was used to estimate the genetic parameters of early growth traits, which can provide the theoretical basis for the breeding of Alpine Merino Sheep in the early stage. 【Method】 Firstly, F- test was performed using ASReml software to determine whether the factors in the fixed effects were significant. And the fixed effects which have significant influence on the early growth traits of Alpine Merino sheep were selected for further analysis. Secondly, four animal models were constructed considering different random effects. And genetic parameters in each model were estimated by the Average Information Restricted Maximum Likelihood (AIREML) in ASReml software. Individual additive genetic effect was considered as random effect in model 1. Besides individual additive genetic effect, maternal genetic effect, individual permanent environmental effect was considered as random effects in model 2 and model3, respectively. Finally, the optimal animal model was selected by comparing the random effects in different models with the Akzo Information Criterion (AIC) Index and Likelihood Ratio Test (LRT). 【Result】 (1) The results showed that bloodline, gender, birth type, birth year, birth month, mating month and flocks highly affected the early growth traits of Alpine Merino sheep (P＜0.001). Except gender and birth type, other fixed effects were significant on gestation length (P＜0.001). (2) The direct heritabilities were (0.0924±0.0160)-(0.2073±0.0226), (0.0651±0.0126)-(0.1027±0.0159), (0.0681±0.0130)-(0.1001±0.1061), (0.0865±0.0148)- (0.0937±0.0149) and (0.0902±0.0174)-(0.1119±0.0189) for BWT, WWT, ADG, WSL, GL, respectively. The maternal heritabilities were 0.1623±0.0113, (0.1097±0.0407)-(0.1098±0.0112), 0.0898±0.0112, 0.0173±0.0107 and 0.0477±0.0146 for birth weight (BWT), weaning weight (WWT), pre-weaning average daily gain (ADG), weaning staple length (WSL) , gestation length (GL), respectively. (3) The comparative analysis of the random effects in different models by the Akaike information criterion (AIC ) and the likelihood ratio test (LRT) showed that the early growth traits were significantly affected by the individual additive genetic effects and maternal genetic effects, but the individual permanent environmental effects were negligible. Therefore, the model 2 was the best model for the early growth traits of Alpine Merino Sheep. 【Conclusion】 The early growth traits of Alpine Merino Sheep were affected by maternal genetic effects more than other random effects. Model 2 was the best animal model for estimating the genetic parameters of early growth traits of Alpine Merino Sheep. Based on the best animal model, the direct heritabilities were 0.0924 ± 0.0160, 0.0651 ± 0.0126, 0.0681 ± 0.0130, 0.0865 ± 0.0148, 0.0902 ± 0.0174 for BWT, WWT, ADG, WSL, GL, respectively. The maternal heritabilities of these traits were 0.1623 ± 0.0113, 0.1098 ± 0.0112, 0.0898 ± 0.0112, 0.0173 ± 0.0107 and 0.0477 ± 0.0146, respectively.

Genome-Wide Association of Spleen Weight in Layer Chicken

SHEN ManMan, QU Liang, DOU TaoCun, MA Meng, GUO Jun, LU Jian, HU YuPing, LI YongFeng, WANG KeHua

Scientia Agricultura Sinica. 2018, 51(6):  1213-1222.  doi:10.3864/j.issn.0578-1752.2018.06.019

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【Objective】 Genome-wide association study (GWAS) was used to demonstrate the molecular mechanism and genetic architecture of chicken spleen weight, which will provide a basis for improving hens health condition in late laying period. 【Method】 The resource population was from reciprocal by Dongxiang Blueshell Chicken and White Leghon, the spleen weight of 1 501 individuals from F2 generation was used as the experimental material. First, the F2 population genome DNA was genotyped by 600 K Affymetrix Axiom Chicken Genotyping Array. Then the quality control was conducted by APT software, some sporadic missing genotypes were imputed using BEAGLE procedure, principal component analysis was performed by PLINK software, genome-wide association study was carried out by GEMMA software, after these steps, the significant and suggestive loci association with spleen weight was identified. Besides, the heritability of spleen weight and chromosome was calculated by GCTA software. According to the false positive significant or suggestive loci, conditional analysis was carried out with the leading SNP as covariance and the linkage disequilibuium was analysis by Haploview. Eventually, the candidate genes were identified based on the gene annotation. 【Result】The phenotype of spleen weight showed extensive variations in late laying period. The heritability of spleen weight was 0.236. A total of 435 867 high quality SNPs were obtained after genotyped. The genomic inflation factor was 1.042 which showed that there is negligible inflation caused by population stratification. Totally, we found 412 and 281 SNPs for significant and suggestive association with spleen weight, respectively. The SNPs that located on GGA1 (gallus gallus chromosome 1), GGA4, GGA16 and GGA28, the significant region on GGA1 spanned from 161 to 174 Mb and ranged from 0.47 to 1.27 on GGA28, the suggestive significant SNPs located on 76 Mb on GGA4 and 175 kb on GGA16. Due to the linkage disequilibrium between the significant loci, the conditional analysis and linkage disequilibrium were performed. After conditional analysis of rs314001986 on GGA1 and rs312729296 on GGA28, the significant loci all dropped below threshold. The linkage disequilibrium analysis was performed by the significant loci on GGA4 and GGA16, the results showed that the suggestive loci showed strong linkage disequilibrium. The genes KCTD4, LDB2, HEP21, and PCASP2 that may involve in spleen growth development and immune response were considered as candidate gene after blasting against chicken genome reference assembly. Moreover, the heritability based on SNP of GGA1 was 9.25%, GGA28 was 4.55%. 【Conclusion】These results enriched the genetic architecture for spleen weight of adult hen in late laying period, the heritability of spleen weight was novel. By bioinformatics analysis the QTL detected for spleen weight was also novel, and 4 candidate genes identified.