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1. 基于单个或多个品种参考群体评估影响猪基因型填充准确性的因素
ZHANG Kai-li, PENG Xia, ZHANG Sai-xian, ZHAN Hui-wen, LU Jia-hui, XIE Sheng-song, ZHAO Shu-hong, LI Xin-yun, MA Yun-long
Journal of Integrative Agriculture    2022, 21 (2): 486-495.   DOI: 10.1016/S2095-3119(21)63695-X
摘要281)      PDF    收藏

基因型填充已成为基因组分析中预处理的关键步骤,其准确性直接影响下游分析。许多因素都会影响填充的准确性,其中,混合参考群体的填充倍受关注。这项研究旨在:评估填充及其影响因素之间的关系,以确保更高的填充精度;探索在参考群体中包含多个品种(系)是否有利于猪填充的准确性;选择具有良好填充效果的填充软件。在这项研究中我们使用50K芯片数据,基于单品系(大白A系)和多品种(大白A系,大白B系,杜洛克长白)参考群体评估了填充精度随验证群体标记密度参考群体样本量最小等位基因频率和参考群体组成四种影响因素的变化,并比较了Beagle 4.1、FImpute、IMPUTE2 MaCH-Admix四种填充软件的填充准确率和运行时间。通过计算填充后SNPs和真实SNPs间的基因型一致率和皮尔森相关性获得填充精度。首先,我们通过随机缺失验证群体中20、45、70、95%和99%的SNPs来模拟低密度芯片,以研究标记密度的影响。然后,我们从原参考群体中随机抽取8、86、173、434868头猪作为新的参考群体来研究参考群体样本量对填充精度的作用。对于最小等位基因频率,SNPs等位基因频率被分为7类,分别计算每类SNPs的填充准确性。结果显示,随着验证群体标记密度,参考群体样本量和最小等位基因频率增加,填充准确增加。当参考群体为与验证群体品系一致的单品系群体时,填充准确性较高,其他品种(系)的添加会导致相对差的填充结果。此外,随着参考群体中主效品系样本量的增加,填充准确性也会提高。在所有填充情景中,综合考虑填充精度和运行时间,Beagle 4.1FImpute优于IMPUTE2 MaCH-Admix。这项工作使从事相关研究的人员能够更直观地了解这些影响因素对填充的影响,并为实际猪育种中实施填充策略提供实践指导。

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2.
Higher leaf area through leaf width and lower leaf angle were the primary morphological traits for yield advantage of japonica/indica hybrids
WEI Huan-he, YANG Yu-lin, SHAO Xing-yu, SHI Tian-yi, MENG Tian-yao, LU Yu, TAO Yuan, LI Xin-yue, DING En-hao, CHEN Ying-long, DAI Qi-gen
Journal of Integrative Agriculture    2020, 19 (2): 483-494.   DOI: 10.1016/S2095-3119(19)62628-6
摘要143)      PDF    收藏
The yield potential of japonica/indica hybrids (JIH) has been achieved over 13.5 t ha–1 in large-scale rice fields, and some physiological traits for yield advantage of JIH over japonica inbred rice (JI) and indica hybrid rice (IH) were also identified.  To date, little attention has been paid to morphological traits for yield advantage of JIH over JI and IH.  For this reason, three JIH, three JI, and three IH were field-grown at East China (Ningbo, Zhejiang Province) in 2015 and 2016.  Compared with JI and IH, JIH had 14.3 and 20.8% higher grain yield, respectively, attributed to its more spikelets per panicle and relatively high percentage of filled grains.  The advantage in spikelets per panicle of JIH over JI and IH was shown in number of grains on the upper, middle, and lower branches.  Compared with JI and IH, JIH had higher leaf area through leaf width and lower leaf angle of upper three leaves, higher leaf area index and leaf area per tiller at heading and maturity stages, higher stem weight per tiller and K and Si concentrations of stem at maturity, higher dry matter weight in leaf, stem, and panicle at heading and maturity stages, and higher biomass accumulation after heading and lower biomass translocation from stem during ripening.  Leaf width of upper three leaves were correlated positively, while leaf angle of upper three leaves were correlated negatively with biomass accumulation after heading, stem weight per tiller, and per unit length.  Our results indicated that the grain yield advantage of JIH was ascribed mainly to the more spikelets per panicle and relatively high percentage of filled grains.  Higher leaf area through leaf width and more erect leaves were associated with improved biomass accumulation and stem weighing during ripening, and were the primary morphological traits underlying higher grain yield of JIH.
 
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3. Morpho-physiological traits contributing to better yield performance of japonica/indica hybrids over indica hybrids under input-reduced practices
WEI Huan-he, MENG Tian-yao, GE Jia-lin, ZHANG Xu-bin, LU Yu, LI Xin-yue, TAO Yuan, DING En-hao, CHEN Ying-long, DAI Qi-gen
Journal of Integrative Agriculture    2020, 19 (11): 2643-2655.   DOI: 10.1016/S2095-3119(20)63251-8
摘要122)      PDF    收藏
It is widely reported that japonica/indica hybrids (JIH) have superior grain yield over other main varietal groups such as indica hybrids (IH) under sufficient resource inputs.  To date, little attention has been paid to yield performance of JIH under input-reduced practices, and whether JIH could have better grain yield performance over IH under input-reduced practices.  In this study, three JIH varieties and three IH varieties were compared in grain yield and their related morpho-physiological traits under two cultivation modes, i.e., conventional high-yielding method (CHYM) and double reductions in nitrogen rate and planting density (DRNP).  Our results showed that JIH had 8.3 and 13.3% higher grain yield over IH under CHYM and DRNP, respectively.  The superior grain yield of JIH over IH under DRNP was mainly attributed to larger sink size and improved sink filling efficiency.  Three main morpho-physiological traits were concluded for better yield performance of JIH over IH under DRNP.  Firstly, JIH had the reduced unproductive tillers growth, indicated by a higher percentage of productive tillers and the percentage of effective leaf area index (LAI) to total LAI at heading stage.  Secondly, a synergistic increase in biomass accumulation and harvest index were achieved of JIH, supported by higher biomass accumulation and leaf area duration during the main growth periods, and improved non-structural carbohydrate (NSC) remobilization after heading.  Thirdly, JIH had an improved canopy structure, showing as higher leaf area of upper three leaves and lower light extinction coefficient.  Our results suggested that improved morpho-physiological traits of JIH could lead to better grain yield performance over IH under input-reduced practices.
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4. Inducible overexpression of porcine homeobox A10 in the endometrium of transgenic mice
LIN Rui-yi, WU Di, ZHAO Chang-zhi, CHEN Shang-shang, XIAO Qian, LI Xin-yun, ZHAO Shu-hong
Journal of Integrative Agriculture    2016, 15 (06): 1338-1344.   DOI: 10.1016/S2095-3119(15)61169-8
摘要1745)      PDF    收藏
   Homeobox A10 (HOXA10) is a well-known transcription factor that plays an important role in directing endometrial differentiation and establishing the conditions required for implantation. Interestingly, the expression level of HOXA10 may be associated with litter size. To study the effects of the porcine HOXA10 promoter fragment on the expression of HOXA10 gene in vivo, we generated a transgenic mouse model using pronuclear microinjection, and measured the expression of HOXA10 in the endometrium. There was no difference in the expression level of HOXA10 between transgenic and wild-type mice in the absence of hormone stimulation. However, following treatment with progesterone and estradiol benzoate, the expression level of HOXA10 was significantly increased in transgenic mice compared with that of wild-type mice. Furthermore, the litter size of transgenic females was larger than that of wild-type females (7.02±1.73 vs. 6.48±1.85; P=0.14). Moreover, the difference of litter size was greater in the later parities (7.33±1.62 vs. 6.37±2.02; P=0.08) compared with the first parity (6.76±1.81 vs. 6.61±1.67; P=0.77) between transgenic and wild-type mice. Therefore, our transgenic mouse model provides exciting insights regarding the actions of HOXA10 and its hormone-inducible promoter in vivo. The present study offers valuable proof of principle to develop transgenic pigs with a hormone-inducible promoter regulating HOXA10 to alter litter size.
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5. Analysis of the Genetic Diversity and Origin of Some Chinese Domestic Duck Breeds
ZHANG Yang, CHEN Yang, ZHEN Ting, HUANG Zheng-yang, CHEN Chang-yi, LI Xin-yu
Journal of Integrative Agriculture    2014, 13 (4): 849-857.   DOI: 10.1016/S2095-3119(13)60447-5
摘要1761)      PDF    收藏
Twelve fluorescence-labeled microsatellite markers were used to analyze the genetic diversity of 12 domestic duck breeds and 2 wild duck breeds to determine the relationship and origin of Chinese domestic duck breeds. Gene frequency, effective number of alleles (Ne), expected heterozygosity (He), polymorphism information contents (PIC), inbreeding coefficient in population (Fis), standard genetic distance (DS), and genetic distance (DA) were calculated by FSTAT and distance and phylogenetic analysis after the dates which were output from the Microsatellite-Toolkit software. Genetic distances between 12 domestic duck breeds and 2 wild duck breeds were analyzed by variance analysis. Unweighted pair group method with arithmetic mean (UPGMA) and phylogenetic trees used for cluster analysis were structured. The results indicated that 11 loci had medium- or high-level genetic diversity among the 12 loci, which could be efficiently used in the detection of the genetic parameters of each population. The values of He were 0.5414 to 0.7343, those of PIC proved similar, and those of Fis were 0.1101 to 0.3381 among all populations. All breeds were clustered into three groups by UPGMA phylogenetic trees. Banzui duck was clustered into a separate group. Differences of the DA were analysed by t-test. The results showed that difference in DA between the 12 domestic duck breeds and Lvtou duck and the Banzui duck were very significant (P<0.01), indicating that these 12 domestic duck breeds originated from Lvtou wild duck, but not Banzui duck.
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