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Coincidence in map positions between pathogen-induced defense-responsive genes and quatitative resistance loci in rice

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Science China(Life Sciences) 2002年第5期45卷 518-526页

作者：熊敏王石平张启发 1. National key laboratory of crop genetic improvement National Center of Crop Molecular Breeding Huazhong Agricultural University 430070 Wuhan China

Quantitative disease resistance conferred by quantitative trait loci (QTLs) is presumably of wider spectrum and durable. Forty-four cDNA clones, representing 44 defense-responsive genes, were fine mapped to 56 loci distributed on 9 of the 12 rice chromosomes. The locations of 32 loci detected by 27 cDNA clones were associated with previously identified resistance QTLs for different rice diseases, including blast, bacterial blight, sheath blight and yellow mottle virus. The loci detected by the same multiple-copy cDNA clones were frequently located on similar locations of different chromosomes. Some of the multiple loci detected by the same clones were all associated with resistance QTLs. These results suggest that some of the genes may be important components in regulation of defense responses against pathogen invasion and they may be the candidates for studying the mechanism of quantitative disease resistance in rice.

关键词： QTL, disease resistance, mapping, rice.

genetic architecture of embryo size and related traits in maize

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The crop Journal 2022年第1期10卷 204-215页

作者： Xiaowei Li Min Wang Renyu Zhang Hui Fang Xiuyi Fu Xiaohong Yang Jiansheng Li State key laboratory of Plant Physiology and Biochemistry National Maize Improvement Center of ChinaMOA Key Laboratory of Maize BiologyBeijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing 100193China

The embryo in maize has a critical role in controlling kernel nutrition components and grain *** measured five embryo weight and size traits,six kernel weight and size traits,and five embryo-tokernel ratio traits in a nested association mapping(NAM)population of 611 recombinant inbred lines(RILs)derived from four inbred lines including the high-oil,giant-embryo line BY815 as the common *** three statistical methods,we identified 5–22 quantitative trait loci(QTL)for each trait,explaining 4.7%–46.7%of the phenotypic *** genetic architecture of maize embryo size and its related traits appeared to be dominated by multiple small-effect loci with little epistasis,and the genetic control underlying embryo size appeared to be distinct from that underlying kernel size.A trait–QTL association network included 205 nodes and 439 edges and revealed 28 key loci associated with at least three *** maize genes including Zm Urb2,Emp12 and Zm BAM1 d,maize orthologs of known rice genes that control seed size including BG1,XIAO and GS9,and 11 maize orthologs of Arabidopsis EMBRYO-DEFECTIVE(EMB)genes were identified as underlying these key ***,the phenotypic and genetic relationships between embryo size and kernel size were evaluated,and genetic patterns for identified loci that control embryo size and its related traits were *** findings reveal distinct genetic architectures for embryo size,kernel size,and embryo-to-kernel ratio traits and establish a foundation for the improvement of embryo-size-mediated kernel nutrition and grain yield.

关键词： Embryo size Kernel size Quantitative trait loci genetic relationship

GS6, A Member of the GRAS Gene Family,Negatively Regulates Grain Size in Rice

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Journal of Integrative Plant Biology 2013年第10期55卷 938-949页

作者： Lianjun Sun Xiaojiao Li Yongcai Fu Zuofeng Zhu Lubin Tan Fengxia Liu Xianyou Sun Xuewen Sun Chuanqing Sun State key laboratory of Plant Physiology and Biochemistry National Center for Evaluation of Agricultural Wild Plants (Rice) MOE Key Laboratory of Crop Heterosis and Utilization key laboratory of crop genetic improvement Department of Plant Genetics and Breeding China Agricultural University State key laboratory of Plant Physiology and Biochemistry National Center for Evaluation of Agricultural Wild Plants(Rice) MOE Key Laboratory of Crop Heterosis and Utilization key laboratory of crop genetic improvement Department of Plant Genetics and Breeding China Agricultural University

Grain size is an important yield-related trait in rice. Intensive artificial selection for grain size during domestication is evidenced by the larger grains of most of today＇s cultivars compared with their wild relatives. However, the molecular genetic control of rice grain size is still not well characterized. Here, we report the identification and cloning of Grain Size 6 （GS6）, which plays an important role in reducing grain size in rice. A premature stop at the ＋348 position in the coding sequence （CDS） of GS6 increased grain width and weight significantly. Alignment of the CDS regions of GS6 in 90 rice materials revealed three GS6 alleles. Most japonica varieties （95%） harbor the Type I haplotype, and 62.9% of indica varieties harbor the Type II haplotype. Association analysis revealed that the Type I haplotype tends to increase the width and weight of grains more than either of the Type II or Type III haplotypes. Further investigation of genetic diversity and the evolutionary mechanisms of GS6 showed that the GS6 gene was strongly selected in japonica cultivars. In addition, a ＂ggc＂ repeat region identified in the region that encodes the GRAS domain of GS6 played an important historic role in the domestication of grain size in rice. Knowledge of the function of GS6 might aid efforts to elucidate the molecular mechanisms that control grain development and evolution in rice plants, and could facilitate the genetic improvement of rice yield.

关键词： Domestication GS6 , grain size haplotype Oryza sativa rice.

Study on the Mitochondrial Genome of Sea Island Cotton(Gossypium barbadense) by BAC Library Screening

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Journal of Integrative Agriculture 2014年第5期13卷 945-953页

作者： SU Ai-guo LI Shuang-shuang LIU Guo-zheng LEI Bin-bin KANG Ding-ming LI Zhao-hu MA Zhi-ying HUA Jin-ping key laboratory of crop Heterosis and Utilization Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology China Agricultural University College of Agronomy Hebei Agricultural University

The plant mitochondrial genome displays complex features, particularly in terms of cytoplasmic male sterility （CMS）. Therefore, research on the cotton mitochondrial genome may provide important information for analyzing genome evolution and exploring the molecular mechanism of CMS. In this paper, we present a preliminary study on the mitochondrial genome of sea island cotton （Gossypium barbadense） based on positive clones from the bacterial artificial chromosome （BAC） library. Thirty-five primers designed with the conserved sequences of functional genes and exons of mitochondria were used to screen positive clones in the genome library of the sea island cotton variety called Pima 90-53. Ten BAC clones were obtained and verified for further study. A contig was obtained based on six overlapping clones and subsequently laid out primarily on the mitochondrial genome. One BAC clone, clone 6 harbored with the inserter of approximate 115 kb mtDNA sequence, in which more than 10 primers fragments could be amplified, was sequenced and assembled using the Solexa strategy. Fifteen mitochondrial functional genes were revealed in clone 6 by gene annotation. The characteristics of the syntenic gene/exon of the sequences and RNA editing were preliminarily predicted.

关键词： Gossypium barbadense BAC library mitochondrial genome RNA editing

Identification and selection of resistance to Bemisia tabaci among 550 cotton genotypes in the field and greenhouse experiments

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Frontiers of Agricultural Science and Engineering 2018年第2期5卷 236-252页

作者： Lizhen ZHU Jianying LI Zhongping XU Hakim MANGHWAR Sijia LIANG Suli LI Muna ALARIQI Shuangxia JIN Xianlong ZHANG National key laboratory of crop genetic improvement Huazhong Agricultural University

Plants have developed sophisticated systems to cope with herbivore challenge, including morphological barriers and secondary metabolites to reduce damage. In this study, 550 Gossypium genotypes were evaluated for whitefly(Bemisia tabaci) resistance in five experiments including two in the field and three in the greenhouse, with23 resistant and 19 susceptible genotypes ***-resistance index determination showed that a leaf having a high density of hairs had resistance to whitfly egg/nymph production. Longer leaf hairs were also important for resistance. This study revealed that okra shaped leaves reduced adult whitefly oviposition preference, while glabrous leaves and high hair density helped not only in the reduction of the adults but also decreased oviposition preference. Gossypol was also observed to be involved in the reduction of adult whitefly development and/or survival.

关键词： Bemisia tabaci Gossypium genotypes gossypol leaf hair density leaf hair length

QTL Identification of the Insensitive Response to Photoperiod and Temperature in Soybean by Association Mapping

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Journal of Integrative Agriculture 2013年第8期12卷 1423-1430页

作者： ZUO Qiao-mei WEN Zi-xiang ZHANG Shu-yun HOU Jin-feng GAI Jun-yi YU De-yue XING Han key laboratory of Biology and genetic improvement of Soybean Ministry of Agriculture/National Key Laboratory of Crop Genetics and Germplasm Enhancement/College of AgricultureNanjing Agricultural University

The insensitive response to photoperiod and temperature is an important quantitative trait for soybean in wide adaptation breeding. The natural variation in response to photoperiod and temperature was detected using 275 accessions of soybean [Glycine max （L.） Merrill] from China. Genome-wide association mapping, based on population structure analysis, was carried out using 118 SSR markers by the TASSEL GLM （general linear model） program. Nine SSR markers （P〈0.01） were associated with the value of the response to photoperiod and temperature （VRPT） caused by days to flowering （DF）, among which, Satt308 （LG M）, Sattl50 （LG M） and Satt440 （LG l）, were identified in both 2006 and 2007. Twelve SSR markers （P〈0.01） were associated with VRPT caused by days to maturity （DM）, among which three markers, Satt387 （LG N）, Satt307 （LG C2） and AW310961 （LG J）, were detected in both 2006 and 2007. In addition, a total of 20 elite alleles were screened out over 2006 and 2007 for being associated with an insensitive response to photoperiod and temperature （IRPT） caused by DF and a total of seven different elite alleles were screened out for being associated with IRPT caused by DM. Among these elite alleles, five alleles, Satt150-244, Satt308-164, Satt308-206, Satt440-176, and Satt440-206, were associated with IRPT caused by DF and were identified in both years, but only one allele, Satt307-170, was identified as being associated with an IRPT caused by DM. Based on these elite alleles, a set of typical accessions were screened out. The result about the genetic basis of IRPT is meaningful for soybean wide adaption breeding.

关键词： QTL association mapping soybean insensitive response photoperiod and temperature

Genome-wide association mapping of stress-tolerance traits in cotton

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The crop Journal 2019年第1期7卷 77-88页

作者： Heng Sun Minghui Meng Zhenhua Yan Zhongxu Lin Xinhui Nie Xiyan Yang National key laboratory of crop genetic improvement Huazhong Agricultural University key laboratory of Oasis Ecology Agricultural of Xinjiang Bingtuan Agricultural College Shihezi University

Environmental stresses severely impair cotton production worldwide. To identify the genetic basis of, and molecular markers associated with, environmental stresses such as salt, cold and Verticillium wilt, association mapping of salt-, cold-, and disease-tolerance traits was performed in a population of 503 upland cotton accessions using 179 polymorphic SSR markers and 11,975 array-derived SNP markers. Salt and cold tolerance was evaluated via the relative germination rate(RGR) of the seeds under seven and four environments, respectively. The disease index of Verticillium wilt was investigated for two years in the field in Xinjiang. These three traits showed large variation across environments. A genome-wide association study revealed that 31, 19, and 15 SSR markers were associated with RGR-Salt(the relative germination rates of seeds under salt stress),RGR-Cold(the relative germination rates of seeds under cold stress), and DIV(the disease index of Verticillium wilt), respectively. Six SNPs in seven environments and two SNPs in BLUP(best linear unbiased prediction) results were associated with RGR-Salt, and the phenotypic variance explained ranged from 3.96 to 5.00%. Two SNPs(i02237 Gh, i02243 Gh)on D01 were concluded to be stable genetic loci associated with RGR-Salt. A total of 223 genes were found in a candidate gene interval(D01, 37771–1942912). Of these four genes,GhPIP3A, GhSAG29, GhTZF4, and GhTZF4a, showed expression changes in sensitive and tolerant genotype accessions under salt stress, and were assigned as candidate genes associated with RGR-Salt. This study revealed the genetic basis of stress resistance in upland cotton and will facilitate stress-resistance breeding in cotton.

关键词： Upland cotton Stress Relative germination rate SSR SNP Candidate gene

Distant eQTLs and Non-coding Sequences Play Critical Roles in Regulating Gene Expression and Quantitative Trait Variation in Maize

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Molecular Plant 2017年第3期10卷 414-426页

作者： Haijun Liu Xin Luo Luyao Niu Yingjie Xiao Lu Chen Jie Liu Xiaqing Wang Minliang Jin Wenqiang Li Qinghua Zhang Jianbing Yan National key laboratory of crop genetic improvement Huazhong Agricultural University Wuhan 430070 China These authors contributed equally to this article

A detailed understanding of genetic architecture of mRNA expression by millions of genetic variants is important for studying quantitative trait variation. In this study, we identified 1.25M SNPs with a minor allele frequency greater than 0.05 by combining reduced genome sequencing （GBS）, high- density array technologies （600K）, and previous deep RNA-sequencing data from 368 diverse inbred lines of maize. The balanced allelic frequencies and distributions in a relatively large and diverse natural panel helped to identify expression quantitative trait loci （eQTLs） associated with more than 18 000 genes （63.4% of tested genes）. We found that distant eQTLs were more frequent （~75% of all eQTLs） across the whole genome. Thirteen novel associated loci affecting maize kernel oil concentration were identified using the new dataset, among which one intergenic locus affected the kernel oil variation by controlling expression of three other known oil-related genes. Altogether, this study provides resources for expanding our understanding of cellular regulatory mechanisms of transcriptome variation and the landscape of functional variants within the maize genome, thereby enhancing the understanding of quantitative variations.

关键词： eQTL RNA-seq GBS GWAS non-coding regulation Zea mays

Development of Oryza rufipogon and O. sativa Introgression Lines and Assessment for Yield-related Quantitative Trait Loci

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Journal of Integrative Plant Biology 2007年第6期49卷 871-884页

作者： Lubin Tan Department of Plant genetics and Breeding and State key laboratory of Agro-biotechnology China Agricultural University Beijing 100094 China key laboratory of crop Heterosis and Utilization of Ministry of Education Beijing 100094 China key laboratory of crop genetic improvement and Genome of Ministry of Agriculture China Agricultural University Beijing 100094 China Beijing key laboratory of crop genetic improvement China Agricultural University Beijing 100094 China

Introgression lines population was effectively used in mapping quantitative trait loci （QTLs）, identifying favorable genes, discovering hidden genetic variation, evaluating the action or interaction of QTLs in multiple conditions and providing the favorable experimental materials for plant breeding and genetic research. In this study, an advanced backcross and consecutive selfing strategy was used to develop introgression lines （ILs）, which derived from an accession of Oryza rufipogon Griff. collected from Yuanjiang County, Yunnan Province of China, as the donor, and an elite indica cultivar Teqing （O. sativa L.）, as the recipient. Introgression segments from O. rufipogon were screened using 179 polymorphic simple sequence repeats （SSR） markers in the genome of each IL. Introgressed segments carried by the introgression lines population contained 120 ILs covering the whole O. rufipogon genome. The mean number of homozygous O. rufipogon segments per introgression line was about 3.88. The average length of introgressed segments was approximate 25.5 cM, and about 20.8% of these segments had sizes less than 10 cM. The genome of each IL harbored the chromosomal fragments of O. rufipogon ranging from 0.54% to 23.7%, with an overall average of 5.79%. At each locus, the ratio of substitution of O. rufipogon alleles had a range of 1.67-9.33, with an average of 5.50. A wide range of alterations in morphological and yield-related traits were also found in the introgression lines population. Using single-point analysis, a total of 37 putative QTLs for yield and yield components were detected at two sites with 7%-20% explaining the phenotypic variance. Nineteen QTLs （51.4%） were detected at both sites, and the alleles from O. rufipogon at fifteen loci （40.5%） improved the yield and yield components in the Teqing background. These O. rufipogon-O, sativa introgression lines will serve as genetic materials for identifying and using favorable genes from common wild rice.

关键词： common wild rice cultivated rice introgression lines quantitative trait locus yield-related trait.