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Molecular characterization of QTL-allele system for drought tolerance at seedling stage and optimal genotype design using multi-locus multi-allele genome-wide association analysis in a half-sib population of soybean (Glycine max (L.) Merr.)

Published online by Cambridge University Press:  23 October 2020

Mueen Alam Khan ,
Fei Tong ,
Wubin Wang ,
Jianbo He ,
Tuanjie Zhao  and
Junyi Gai Open the ORCID record for Junyi Gai [Opens in a new window]
Mueen Alam Khan
Affiliation:
Soybean Research Institute/MARA National Center for Soybean Improvement/MARA Key Laboratory of Biology and Genetic Improvement of Soybean (General)/National Key Laboratory for Crop Genetics and Germplasm Enhancement/Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu210095, China
Fei Tong
Affiliation:
Soybean Research Institute/MARA National Center for Soybean Improvement/MARA Key Laboratory of Biology and Genetic Improvement of Soybean (General)/National Key Laboratory for Crop Genetics and Germplasm Enhancement/Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu210095, China
Wubin Wang
Affiliation:
Soybean Research Institute/MARA National Center for Soybean Improvement/MARA Key Laboratory of Biology and Genetic Improvement of Soybean (General)/National Key Laboratory for Crop Genetics and Germplasm Enhancement/Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu210095, China
Jianbo He
Affiliation:
Soybean Research Institute/MARA National Center for Soybean Improvement/MARA Key Laboratory of Biology and Genetic Improvement of Soybean (General)/National Key Laboratory for Crop Genetics and Germplasm Enhancement/Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu210095, China
Tuanjie Zhao
Affiliation:
Soybean Research Institute/MARA National Center for Soybean Improvement/MARA Key Laboratory of Biology and Genetic Improvement of Soybean (General)/National Key Laboratory for Crop Genetics and Germplasm Enhancement/Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu210095, China
Junyi Gai*
Affiliation:
Soybean Research Institute/MARA National Center for Soybean Improvement/MARA Key Laboratory of Biology and Genetic Improvement of Soybean (General)/National Key Laboratory for Crop Genetics and Germplasm Enhancement/Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu210095, China
*
*Corresponding author. E-mail: sri@njau.edu.cn
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Abstract

Characterizing the whole genetic architecture of drought tolerance (DT) is a persistent challenge for the breeders. Here we developed a half-sib population comprising of 404 lines of two recombinant inbred line (RIL) populations with M8206 as the joint parent (M8206 × TongShan and ZhengYang × M8206) and tested for its DT under sand culture. The population was sequenced using restriction-site-associated DNA sequencing filtered with minor allele frequency ≥0.01; 55,936 single nucleotide polymorphisms (SNPs) were obtained and assembled into 6137 SNPLDBs (SNP linkage disequilibrium blocks). The restricted two-stage multi-locus genome-wide association analysis characterized with error and false-positive control identified 40 QTLs with 93 alleles on an average of 34.75% of the phenotypic variance (PV) collectively for relative root length (RRL) and relative shoot length (RSL) that served as potential DT indicators. Among these, eight loci corresponded to previously reported QTLs, whereas 32 loci were therefore novel. The identified QTLs with their corresponding alleles for RRL and RSL were organized into QTL-allele matrices, depicting the comprehensive DT genetic architecture of the three parents/half-sib population. From the matrices, we predicted the possible best/optimal genotype with weighted average value (WAV) 1.553 over two indicators, while for the top 10 single crosses among RILs with 95th percentile WAV was 1.218–1.257, transgressive over the parents (0.693–0.794) yet much less than 1.553. From the detected QTL-allele system, 65 potential candidate genes collectively for both indicators explaining on an average of 24.41% PV were annotated and χ2-tested as a DT candidate gene system involving nine biological processes.

Keywords

drought tolerancegene annotationsgenome-wide association analysisoptimal cross-designQTL-allele matrixsoybean [Glycine max (L.) Merr.]
Type
Research Article
Information
Plant Genetic Resources , Volume 18 , Issue 5 , October 2020 , pp. 295 - 306
Copyright
Copyright © The Author(s), 2020. Published by Cambridge University Press on behalf of NIAB

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Footnotes

†

The present address: Department of Plant Breeding & Genetics, Faculty of Agriculture & Environment, The Islamia University of Bahawalpur, Bahawalpur, Pakistan

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