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Identification of main effect and epistatic QTLs controlling initial flowering date in cultivated peanut (
Arachis hypogaea
L.)
WANG Liang, YANG Xin-lei, CUI Shun-li, WANG Ji-hong, HOU Ming-yu, MU Guo-jun, LI Zi-chao, LIU Li-feng
2020, 19 (
10
): 2383-2393. DOI:
10.1016/S2095-3119(20)63211-7
Abstract
(
109
)
PDF in ScienceDirect
Initial flowering date (IFD) is closely related to mature period of peanut pods. In present study, a population of recombinant inbred lines (RIL) derived from the cross between Silihong (female parent) and Jinonghei 3 (male parent) was used to map QTLs associated with IFD. The RIL population and its two parental cultivars were planted in two locations of Hebei Province, China from 2015 to 2018 (eight environments). Based on a high-density genetic linkage map (including 2 996 SNP and 330 SSR markers) previously constructed in our laboratory, QTLs were analyzed using phenotypic data and the best linear unbiased prediction (BLUP) value of initial flowering date by inclusive composite interval mapping (ICIM) method. Interaction effects between every two QTLs and between individual QTL and environment were also analyzed. In cultivated peanut, IFD was affected by genotypic factor and environments simultaneously, and its broad sense heritability (h2) was estimated as 86.8%. Using the IFD phenotypic data from the eight environments, a total of 19 QTLs for IFD were detected, and the phenotypic variation explained (PVE) by each QTL ranged from 1.15 to 21.82%. Especially, five of them were also detected by the BLUP value of IFD. In addition, 12 additive QTLs and 35 pairs of epistatic QTLs (62 loci involved) were identified by the joint analysis of IFD across eight environments. Three QTLs (
qIFDB04.1
,
qIFDB07
.
1
and
qIFDB08.1
) located on chromosome B04, B07 and B08 were identified as main-effect QTL for IFD, which had the most potential to be used in peanut breeding. This study would be helpful for the early-maturity and adaptability breeding in cultivated peanut.
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Transcriptome and metabolome profiling of unheading in F
1
hybrid rice
WANG Jie, WEI Shao-bo, WANG Chun-chao, Najeeb Ullah KHAN, ZHANG Zhan-ying, WANG Wen-sheng, ZHAO Xiu-qin, ZHANG Hong-liang, LI Zi-chao, GAO Yong-ming
2020, 19 (
10
): 2367-2382. DOI:
10.1016/S2095-3119(19)62838-8
Abstract
(
140
)
PDF in ScienceDirect
Heading date is a crucial agronomic trait. However, rice usually delays heading due to the photoperiod, temperature, hormones or age. The present research was conducted to analyze the mechanism controlling heading date in F
1
hybrid rice. We constructed two test-crossing populations using two introgression lines (ILs), P20 and P21 coming from SH527/FH838 as the male parent, respectively, and male sterile line Jin23A as the female parent. Meanwhile, the F
1
hybrids of H20, obtained by mating P20 with Jin23A and having no heading, and H21, from the crossing between P21 and Jin23A having normal heading, were both observed under long days. Here, we analyzed the photoperiodic response of F
1
hybrids by transcriptome and metabolome profiling. The greater differences displayed in the transcriptome and the metabolome were caused by photoperiod (exogenous) instead of genes (endogenous). The coping mechanism resulted from long days (LD) in H20, leading to differences in the circadian rhythm and glutathione metabolism relative to other samples. The circadian oscillator and GSH/GSSG cycle typically regulate ROS homeostasis, and both of them are responsible for modulating ROS in H20 under LD condition. Both circadian rhythm genes and the reported genes related to heading date function
via
the
DHD1/OsMFT1-Ehd1-RFT1-OsMADS14/OsMADS18
pathway and the glutathione metabolism pathway by regulating oxidative reduction processes. Both pathways are involved in the heading process and they interacted through the oxidative reduction process which was induced by photoperiod regulation, and all of them collectively modulated the heading process. The results of this study will be helpful for unraveling the mechanism of F
1
hybrid responses to unheading under LD condition.
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Mapping of three QTLs for seed setting and analysis on the candidate gene for qSS-1 in rice (
Oryza sativa
L.)
Elsheikh Y M Ahmed, ZHANG Yan-pei, YU Jian-ping, Rashid M A Rehman, ZHANG Zhan-ying, ZHANG Hong-liang, LI Jin-jie, LI Zi-chao
2016, 15 (
4
): 735-743. DOI:
10.1016/S2095-3119(15)61299-0
Abstract
(
2095
)
PDF in ScienceDirect
The lower seed setting is one of the major hindrances which face grain yield in rice. One of the main reasons to cause low spikelet fertility (seed setting) is male sterility or pollen abortion. Notably, pollen abortion has been frequently observed in advanced progenies of rice. In the present study, 149 BC
2
F
6
individuals with significant segregation in spikelet fertility were generated from the cross between N040212 (
indica
) and Nipponbare (
japonica
) and used for primary gene mapping. Three QTLs,
qSS-1
,
qSS-7
and
qSS-9
at chromosomes 1, 7 and 9, respectively, were found to be associated with seed setting. The recombinant analysis and the physical mapping information from publicly available resources exhibited that the
qSS-1
,
qSS-7
and
qSS-9
loci were mapped to an interval of 188, 701 and 3 741 kb, respectively. The seed setting responsible for QTL
qSS-1
was further fine mapped to 93.5 kb by using BC
2
F
7
population of 1 849 individuals. There are 16 possible putative genes in this 93.5 kb region. Pollen vitality tests and artificial pollination indicated that the male gamete has abnormal pollen while the female gamete was normal. These data showed that low seed setting rate relative to
qSS-1
may be caused by abnormal pollen grains. These results will be useful for cloning, functional analysis of the target gene governing spikelet fertility (seed setting) and understanding the genetic bases of pollen sterility.
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Fine Mapping of qTGW3-1, a QTL for 1000-Grain Weight on Chromosome 3 in Rice
ZHANG Qiang, YAO Guo-xin, HU Guang-long, TANG Bo, ZHANG Hong-liang, LI Zi-chao
2012, 12 (
6
): 879-887. DOI:
10.1016/S1671-2927(00)8610
Abstract
(
1805
)
PDF in ScienceDirect
The QTL qTGW3-1 was located on chromosome 3 of rice (Oryza sativa L.) and associated with the 1 000-grain weight (TGW) according to the result of our earlier study. With the objective of fine mapping of this locus, we developed a F2 population consisting of 3 428 plants derived from the cross between TGW-related near isogenic line DL017 (BC3F4 generation of GSL156×Nipponbare) and the recurrent parent Nipponbare. Using six microsatellites, this QTL was delimited between RM5477 and RM6417. Markers MM1455 and MM1456 within this region were used for further mapping of this QTL. Finally, qTGW3-1 was fine-mapped into a 89-kb interval between RM5477 and MM1456, which locates in the BAC clone AC107226 harboring five putative candidate genes.
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Genetic Structure and Eco-Geographical Differentiation of Cultivated Keng Rice (Oryza sativa L. subsp. japonica) in China Revealed by Microsatellites
ZHANG Dong-ling, WANG Mei-xing, QI Yong-wen, SUNJun-li , WANG Feng-mei, LI Jin-jie, ZHANG Hong-liang, and LI Zi-chao
2012, 12 (
11
): 1755-1766. DOI:
10.1016/S1671-2927(00)8710
Abstract
(
1192
)
PDF in ScienceDirect
China is one of the largest centers of genetic diversity of Oryza sativa L. and is the original centers of Oryza sativa L. subspecies japonica. Using a genetically representative core collection of 1 442 rice landraces of japonica in China, the genetic structure, differentiation, and geographic diversity were analyzed. The model-based structure analysis on varieties within three ecotypes revealed 16 eco-geographical types, which are partially accorded with some of the ecological zones in China. The differentiation of eco-geographical types contributed to the local ecological adaption and physical isolation, and maybe could be used to develop the heterotic groups of japonica. To facilitate the identification of different ecotypes and eco-geographical types, we provided the SSR character alleles of each ecotype or geographical eco-group and a rapid discriminated method based on these character alleles. Lastly, investigation on genetic diversity, genetic differentiation indicated that southwest region of China, including south of Yunnan Province, northwest of Guangxi Zhuang Autonomous Region, and southwest of Guizhou Province, possessed the highest genetic diversity and all the necessary conditions as a center of genetic diversity and should be the center of genetic diversity of rice landraces of japonica in China.
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Fine Mapping and Cloning of the Grain Number Per-Panicle Gene (Gnp4) on Chromosome 4 in Rice (Oryza sativa L.)
ZHANG Zhan-ying, LI Jin-jie, YAO Guo-xin, ZHANG Hong-liang, DOU Hui-jing, SHI Hong-li, SUN Xingming, LI Zi-chao
2011, 10 (
12
): 1825-1833. DOI:
10.1016/S1671-2927(11)60182-X
Abstract
(
2277
)
PDF in ScienceDirect
Grain number per-panicle is one of the most important components for rice yield. Spikelets on the primary and secondary branches determine the grain number per-panicle in rice. In this study, we identified a natural mutant, gnp4, lack of lateral spikelet on the secondary branches in the field condition. In addition, the Gnp4 and Lax1-1 double mutant showed dramatically reduced secondary branches and spikelets in panicle at reproductive stage, and tillers at vegetative stage. By map-based cloning approach, and using four F2 segregating populations, the Gnp4 gene was finally mapped to a 10.7-kb region on the long arm of chromosome 4 in rice. In this region, only one gene was predicted, and genomic DNA sequencing of the 10.7-kb region showed no nucleotide differences between the mutant and wild type. Interestingly, we found that the methylation level of several cytosines in the promoter CpG islands region of the predicted gene in gnp4 were different from the wild type. Thus, we propose that the DNA methylation changes at these sites may induce to decrease expression level of Gnp4, consequently, resulting in phenotypic variation.
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