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Population structure and association mapping to detect QTL controlling tomato spotted wilt virus resistance in cultivated peanuts

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The Crop Journal 2018年第5期6卷 516-526页

作者： Jing Li Yueyi Tang Alana L.Jacobson Phat M.Dang Xiao Li Ming Li Wang Austin Hagan Charles Y.Chen Department of Crop Soil and Environmental SciencesAuburn UniversityAuburnAL 36849USA Shandong Peanut Research Institute Qingdao 266100China Department of Entomology and Plant Pathology Auburn UniversityAuburnAL 36849USA USDA-ARS National Peanut Research Laboratory DawsonGA 39842USA USDA-ARS Plant Genetic Resources Conservation Unit GriffinGA 30223USA

Tomato spotted wilt(TSW)is a serious virus disease of peanut in the United *** for TSWV resistance would be facilitated by the implementation of marker-assisted selection in breeding programs;however,genes associated with resistance have not been *** mapping is a type of genetic mapping that can exploit relationships between markers and traits in many *** objectives of this study were to examine genetic diversity and population structure in the *** mini-core collection using simple sequence repeat(SSR)markers,and to conduct association mapping between SSR markers and TSWV resistance in cultivated *** hundred and thirty-three SSR markers were used for genotyping 104 *** subpopulations,generally corresponding to botanical varieties,were classified by population structure *** mapping analysis indicated that five markers:pP GPseq5D5,GM1135,GM1991,TC23C08,and TC24C06,were consistently associated with TSW resistance by the Q,PCA,Q+K,and PCA+K *** markers together explained 36.4%of the phenotypic ***,pP GPseq5D5 and GM1991 were associated with both visual symptoms of TSWV and ELISA values with a high R^*** potential of these markers for use in a marker-assisted selection program to breed peanut for resistance to TSWV is discussed.

关键词： association mapping SSR markers Tomato spotted wilt virus Peanuts

Genetic and association mapping Study of English Grain Aphid Resistance and Tolerance in Bread Wheat Germplasm

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Journal of Integrative Agriculture 2014年第1期13卷 40-53页

作者： LI Feng-qi PENG Jun-hua Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture Wuhan Botanical GardenChinese Academy of Sciences University of Chinese Academy of Sciences Department of Soil and Crop Sciences Colorado State University

English grain aphid （EGA） is a destructive insect pest of wheat. To identify the loci associated with EGA resistance and tolerance, 70 bread wheat accessions mainly from central Asia were evaluated for EGA resistance and tolerance traits at two locations, and genotyped with 51 SSR markers. Totally, three accessions showed high or moderate levels resistance and 17 genotypes displayed highly or moderately tolerate to EGA. Genetic diversity of these lines was investigated also. After 97 SSR loci which evenly covered all wheat chromosomes were scanned for association, four SSR loci were significantly associated with EGA resistance and four with EGA tolerance. After association analysis was conducted with dynamic aphid densities, we found four loci Xgwm192b, Xgwm391, Xbarc98, and Xgwm613b were detected continuously at different growing stages of wheat. In addition, the loci of EGA resistance/tolerance and Russian wheat aphid resistance were compared. The results generated in this study would be helpful for utilization of the EGA resistance/tolerance germplasm, and for development of mapping populations in EGA resistance breeding programs.

关键词： English grain aphid resistance tolerance association mapping Triticum aestivum

Dissecting the genetic basis of maize deep-sowing tolerance by combining association mapping and gene expression analysis

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Journal of Integrative Agriculture 2022年第5期21卷 1266-1277页

作者： YANG Yue MA Yu-ting LIU Yang-yang Demar LYLE LI Dong-dong WANG Ping-xi XU Jia-liang ZHEN Si-han LU Jia-wen PENG Yun-ling CUI Yu FU Jun-jie DU Wan-li ZHANG Hong-wei WANG Jian-hua Agronomy College Shenyang Agricultural UniversityShenyang 110161P.R.China National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences Chinese Academy of Agricultural SciencesBeijing 100081P.R.China Center for Seed Science and Technology College of Agronomy and BiotechnologyChina Agricultural UniversityBeijing 100193P.R.China Gansu Provincial Key Laboratory for Aridland Crop Science/Agronomy College Gansu Agricultural UniversityLanzhou 730070P.R.China

Deep-sowing is an important method for avoiding drought stress in crop species,including *** candidate genes is the groundwork for investigating the molecular mechanism underlying maize deep-sowing *** study evaluated four traits(mesocotyl length at 10 and 20 cm planting depths and seedling emergence rate on days 6 and 12)related to deep-sowing tolerance using a large maize population containing 386 inbred lines genotyped with 0.5 million high-quality single nucleotide polymorphisms(SNPs).The genomewide association study detected that 273 SNPs were in linkage disequilibrium(LD)with the genetic basis of maize deep-sowing *** RNA-sequencing analysis identified 1944 and 2098 differentially expressed genes(DEGs)in two comparisons,which shared 281 *** comparing the genomic locations of the 273 SNPs with those of the 281 DEGs,we identified seven candidate genes,of which GRMZM2G119769 encoded a sucrose non-fermenting 1 kinase interactor-like ***2G119769 was selected as the candidate gene because its homologs in other plants were related to organ length,auxin,or light *** gene association mapping revealed that natural variations in GRMZM2G119769 were related to phenotypic variations in maize mesocotyl *** expression of GRMZM2G119769 was higher in deep-sowing tolerant inbred *** results suggest that GRMZM2G119769 is the most likely candidate *** study provides information on the deep-sowing tolerance of maize germplasms and identifies candidate genes,which would be useful for further research on maize deep-sowing tolerance.

关键词： maize mesocotyl length association mapping differentially expressed gene SNF1 kinase interactor-like protein

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

Genotype × Environment Interactions for Agronomic Traits of Rice Revealed by association mapping

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Rice science 2014年第3期21卷 133-141页

作者： XU Fei-fei TANG Fu-fu SHAO Ya-fang CHEN Ya-ling TONG Chuan BAO Jin-song Institute of Nuclear Agricultural Sciences College of Agriculture and BiotechnologyHuajiachi CampusZhejiang University

Agronomic traits are important determinants to rice yield, which are controlled by complex genetic factors as well as genotype by environment （G × E） interaction effects. The G × E effects for agronomic traits of rice have been dissected with various approaches, but not with the current available approach, the association studies. In this study, a total of 32 655 single nucleotide polymorphisms were used to carry out associations with 14 agronomic traits among 20 rice accessions in two environments. The G × E interaction effects for all the agronomic traits were at highly significant levels （P〈0.01）, accounting for 3.4%-22.3% of the total sum of squares except for the length of brown rice. Twenty three putative quantitative trait loci （QTLs）, including five previously known and several new promising associations, were identified for 10 of 14 traits. Analysis of the relationships between the traits for which QTLs and the genotype effects could be identified suggested that the higher the genotypic effect, the higher the possibility to identify QTLs for the given trait. The new QTLs detected in this study will facilitate dissection of the complex agronomic traits and may give insight into the G × E effects with association mapping.

关键词： rice yield agronomic trait association mapping single nucleotide polymorphism

association mapping for enhancing maize genetic improvement

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Association mapping for enhancing maize genetic improvement

第十四届全国植物基因组学大会

作者： Jianbing Yan National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural University

association mapping through linkage disequilibrium(LD) analysis is a powerful tool for the dissection of complex agronomic traits and for the identification of alleles that can contribute to the enhancement of a target *** the developments of high throughput genotyping techniques and advanced statistical approaches as well as the assembling and characterization of multiple association mapping panels,maize has

关键词： maize association mapping genetic architecture RNA-Seq quantitative traits

Linkage Disequilibrium in a Diversity and Stress Adaptation Rice Panel for association mapping

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Linkage Disequilibrium in a Diversity and Stress Adaptation ...

中国作物学会2013年学术年会

作者： XIAO Yu-Long YU Chuan-Yuan Jonalyn M.YABES LEI Jian-Guo WANG Xiao-Ling WANG Zhi-Quan CHEN Hong-Ping Dindo A.TABANAO Rice Research Institute JiangXi Academy of Agricultural Science

Estimated of linkage disequilibrium(LD) are important as an indication of how useful LD-base association genetics approaches can be when compared with other available mapping *** success of association mapping efforts depends on the possibilities of separating LD due to linkage from LD due to other *** an attempt to associate markers with drought tolerance at vegetative stage,we examined the pattern of LD in a diversity and stress adaptation rice panel containing 184 rice germplasm accessions with 141 polymorphic SSR markers that were nearly evenly distributed at 3mb bin on the 12 rice *** LD was detected across the genome of the 184 rice genotypes and the extent of LD varied with different chromosomes, selfing in *** species and existing of population structure in the rice panel might be the major factors of creating high *** genetic linkage was detected except for two pairs of SSR markers RM288 and RM464 (11.98758 Mb),RM215 and RM464(14.61396 Mb),which were located on chromosome 9 at a relatively far distance but showed significantly higher *** high degree of LD and fast decay of LD detected in this experiment indicating the 141 SSR markers used in the experiment could be feasible to carry out the whole-genome scan association studies with a relatively high resolution.

关键词： linkage disequilibrium(LD) LD Decay rice association mapping

Identification of Sicl1 gene controlling leaf curling and capsule indehiscence in sesame via cross-population association mapping and genomic variants screening

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Identification of Sicl1 gene controlling leaf curling and ca...

中国作物学会油料作物专业委员会第八次会员代表大会暨学术年会

作者： ZHANG Hai-yang MIAO Hong-mei WEI Li-bin LI Chun DUAN Ying-hui XU Fang-fang QU Wen-wen ZHAI Rui-hong JU Ming CHANG Shu-xian Henan Sesame Research Center Henan Academy of Agricultural Sciences

Leaf shape can affect the plantlet development in *** we performed morphological and genetic analysis of a mutant cl1(cl) with curly leaf and indehiscent capsule *** cl1,the parenchyma cells in the leaf blades reduced the adaxial/abaxial *** leaf curling trait is controlled by a regressive gene(Sicl1).Cross-population association of the 130 individuals of cl1 × USA(0)-26 F population indicated that the target cl locus was located in the interval C29 between C29522236 and C29918901 in Si *** on the validation of the integrated marker SiCLInDel1(C29:6721553-6721572) in cl1 X Yuzhi 11 F population and accessions,C29.460 was proved the target gene SiCL1 in *** is a KANl homolog with the full length of 6 635 ***,Sicll shortened to 1 829 *** cl1,The 20 nucleic acids of SiCLInDel1 marker were mutagenized into 6 nucleic *** deletion led to a frameshift mutation and finally resulted in the earlier translation *** findings provided an example of high-efficient gene cloning in sesame.

关键词： Sesamum indicum L. curly leaf indehiscent capsule association mapping KAN1

Genetic Dissection of Eating and Cooking Qualities in Different Subpopulations of Asian Cultivated Rice(Oryza sativa L.) through association mapping

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Genetic Dissection of Eating and Cooking Qualities in Differ...

第十九届中国作物学会学术年会

作者：赵春芳 Ling Zhao Qingyong Zhao Tao Chen Shu Yao Zhen Zhu Lihui Zhou Altafhusian B.Nadaf Wenhua Liang Kai Lu Yadong Zhang 王才林 Institute of Food Crops Jiangsu Academy of Agricultural Sciences Jiangsu Rice Engineering Research Center National Center for Rice Improvement (Nanjing)

[Background] Eating and cooking qualities(ECQs) of rice(Oryza sativa L.) determine consumer acceptance and the economic value of rice varieties. Genetic factors are required for development of rice varieties with excellent ECQs and association mapping is one of the promising approaches for discovering such associated genetic factors. [Material and method] A genome-wide association mapping was performed on a set of 253 non-glutinous rice accessions consisting of 83 indica and 170 japonica Asian cultivated rice varieties through phenotyping for 11 ECQ traits in two consecutive years and genotyping with 210 polymorphic SSR and candidate-gene markers. [Results] These markers amplified 747 alleles with an average of 3.57 alleles per locus. The structure, phylogenetic relationship, and principal component analysis indicated a strong population differentiation between indica and japonica accessions and association mapping was thus undertaken within indica and japonica subpopulations. All traits showed a large phenotypic variation and highly significant phenotypic correlations were present between most of traits. A total of 33 and 30 loci were located for 11 ECQs in indica and japonica subpopulations respectively. Most of associated loci were overlapped with starch synthesis-related genes(SSRGs), and the Wx locus gathered 14 associated loci with the largest effects on amylose content, gel consistency and pasting viscosities. Eight subpopulation specific markers, RM588, Wx-(CT)n, SSI and SBE1 for indica subpopulation and RM550, Wxmp, SSIIa and SBE4 for japonica subpopulation, were identified, suggesting alleles of SSRGs showed the subspecific tendency. Nevertheless, allelic variation in SSIIa showed no tendency towards subspecies. One associated maker RM550 detected in japonica subpopulation for amylose content and pasting viscosity was verified a potential novel and stably expressed locus and also indicated selection for further fine mapping. [Conclusion] This study illustr

关键词： rice(Oryza sativa L.) eating and cooking quality subpopulation association mapping