Whole-genome mapping identified novel “QTL hotspots regions” for seed storability in soybean ( Glycine max  L.)

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Abstract

Background

Seed aging in soybean is a serious challenge for agronomic production and germplasm preservation. However, its genetic basis remains largely unclear in soybean. Unraveling the genetic mechanism involved in seed aging, and enhancing seed storability is an imperative goal for soybean breeding. The aim of this study is to identify quantitative trait loci (QTLs) using high-density genetic linkage maps of soybean for seed storability. In this regard, two recombinant inbred line (RIL) populations derived from Zhengyanghuangdou × Meng 8206 (ZM6) and Linhefenqingdou × Meng 8206 (LM6) crosses were evaluated for three seed-germination related traits viz., germination rate (GR), normal seedling length (SL) and normal seedling fresh weight (FW) under natural and artificial aging conditions to map QTLs for seed storability.

Results

A total of 34 QTLs, including 13 QTLs for GR, 11 QTLs for SL and 10 QTLs for FW, were identified on 11 chromosomes with the phenotypic variation ranged from 7.30 to 23.16% under both aging conditions. All these QTLs were novel, and 21 of these QTLs were clustered in five QTL-rich regions on four different chromosomes viz., Chr3, Chr5, Chr17 &Chr18, among them the highest concentration of seven and six QTLs were found in “QTL hotspot A” (Chr17) and “QTL hotspot B” (Chr5), respectively. Furthermore, QTLs within all the five QTL clusters are linked to at least two studied traits, which is also supported by highly significant correlation between the three germination-related traits. QTLs for seed-germination related traits in “QTL hotspot B” were found in both RIL populations and aging conditions, and also QTLs underlying “QTL hotspot A” are identified in both RIL populations under artificial aging condition. These are the stable genomic regions governing the inheritance of seed storability in soybean, and will be the main focus for soybean breeders.

Conclusion

This study uncovers the genetic basis of seed storability in soybean. The newly identified QTLs provides valuable information, and will be main targets for fine mapping, candidate gene identification and marker-assisted breeding. Hence, the present study is the first report for the comprehensive and detailed investigation of genetic architecture of seed storability in soybean.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5897-5) contains supplementary material, which is available to authorized users.

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Most cited references 59

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J D Bewley (1997)

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High-throughput genotyping by whole-genome resequencing.

Xuehui Huang, Qi Feng, Qian Qian … (2009)

The next-generation sequencing technology coupled with the growing number of genome sequences opens the opportunity to redesign genotyping strategies for more effective genetic mapping and genome analysis. We have developed a high-throughput method for genotyping recombinant populations utilizing whole-genome resequencing data generated by the Illumina Genome Analyzer. A sliding window approach is designed to collectively examine genome-wide single nucleotide polymorphisms for genotype calling and recombination breakpoint determination. Using this method, we constructed a genetic map for 150 rice recombinant inbred lines with an expected genotype calling accuracy of 99.94% and a resolution of recombination breakpoints within an average of 40 kb. In comparison to the genetic map constructed with 287 PCR-based markers for the rice population, the sequencing-based method was approximately 20x faster in data collection and 35x more precise in recombination breakpoint determination. Using the sequencing-based genetic map, we located a quantitative trait locus of large effect on plant height in a 100-kb region containing the rice "green revolution" gene. Through computer simulation, we demonstrate that the method is robust for different types of mapping populations derived from organisms with variable quality of genome sequences and is feasible for organisms with large genome sizes and low polymorphisms. With continuous advances in sequencing technologies, this genome-based method may replace the conventional marker-based genotyping approach to provide a powerful tool for large-scale gene discovery and for addressing a wide range of biological questions.

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Multiplexed shotgun genotyping for rapid and efficient genetic mapping.

Peter Andolfatto, Dan Davison, Deniz Erezyilmaz … (2011)

We present a new approach to genotyping based on multiplexed shotgun sequencing that can identify recombination breakpoints in a large number of individuals simultaneously at a resolution sufficient for most mapping purposes, such as quantitative trait locus (QTL) mapping and mapping of induced mutations. We first describe a simple library construction protocol that uses just 10 ng of genomic DNA per individual and makes the approach accessible to any laboratory with standard molecular biology equipment. Sequencing this library results in a large number of sequence reads widely distributed across the genomes of multiplexed bar-coded individuals. We develop a Hidden Markov Model to estimate ancestry at all genomic locations in all individuals using these data. We demonstrate the utility of the approach by mapping a dominant marker allele in D. simulans to within 105 kb of its true position using 96 F1-backcross individuals genotyped in a single lane on an Illumina Genome Analyzer. We further demonstrate the utility of our method by genetically mapping more than 400 previously unassembled D. simulans contigs to linkage groups and by evaluating the quality of targeted introgression lines. At this level of multiplexing and divergence between strains, our method allows estimation of recombination breakpoints to a median of 38-kb intervals. Our analysis suggests that higher levels of multiplexing and/or use of strains with lower levels of divergence are practicable.

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Author and article information

Contributors

Xi Zhang: xx726175067@qq.com

Aiman Hina: aimanhina@yahoo.com

Shiyu Song: zz835@sina.cn

Jiejie Kong: 2012094@njau.edu.cn

Javaid Akhter Bhat: javid.akhter69@gmail.com

Tuanjie Zhao: tjzhao@njau.edu.cn

Journal

Journal ID (nlm-ta): BMC Genomics

Journal ID (iso-abbrev): BMC Genomics

Title: BMC Genomics

Publisher: BioMed Central (London )

ISSN (Electronic): 1471-2164

Publication date (Electronic): 17 June 2019

Publication date PMC-release: 17 June 2019

Publication date Collection: 2019

Volume: 20

Electronic Location Identifier: 499

Affiliations

ISNI 0000 0000 9750 7019, GRID grid.27871.3b, Soybean Research Institution, National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, , Nanjing Agricultural University, ; Nanjing, 210095 China

Article

Publisher ID: 5897

DOI: 10.1186/s12864-019-5897-5

PMC ID: 6580613

PubMed ID: 31208334

SO-VID: 0ecdf484-b34a-4459-bef9-59a18b8b69ec

License:

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

History

Date received : 6 November 2018

Date accepted : 11 June 2019

Funding

Funded by: FundRef http://dx.doi.org/10.13039/501100001809, National Natural Science Foundation of China;

Award ID: 31571691 and 31871646

Award Recipient : Tuanjie Zhao

Custom metadata

ScienceOpen disciplines: Genetics

Keywords: qtl,seed storability,high-density linkage map,seed aging,soybean

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ScienceOpen disciplines: Genetics

Keywords: qtl, seed storability, high-density linkage map, seed aging, soybean

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Whole-genome mapping identified novel “QTL hotspots regions” for seed storability in soybean ( Glycine max L.)

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Abstract

Background

Results

Conclusion

Electronic supplementary material

Related collections

Genome Integrity

Most cited references 59

Seed Germination and Dormancy.

High-throughput genotyping by whole-genome resequencing.

Multiplexed shotgun genotyping for rapid and efficient genetic mapping.

Author and article information

Contributors

Journal

Affiliations

Article

History

Funding

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Cited by 14

Most referenced authors 2,386