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      Construction of high-density genetic map and QTL mapping of yield-related and two quality traits in soybean RILs population by RAD-sequencing

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          Abstract

          Background

          One of the overarching goals of soybean breeding is to develop lines that combine increased yield with improved quality characteristics. High-density-marker QTL mapping can serve as an effective strategy to identify novel genomic information to facilitate crop improvement. In this study, we genotyped a recombinant inbred line (RIL) population (Zhonghuang 24 × Huaxia 3) using a restriction-site associated DNA sequencing (RAD-seq) approach. A high-density soybean genetic map was constructed and used to identify several QTLs that were shown to influence six yield-related and two quality traits.

          Results

          A total of 47,472 single-nucleotide polymorphisms (SNPs) were detected for the RILs that were integrated into 2639 recombination bin units, with an average distance of 1.00 cM between adjacent markers. Forty seven QTLs for yield-related traits and 13 QTLs for grain quality traits were found to be distributed on 16 chromosomes in the 2 year studies. Among them, 18 QTLs were stable, and were identified in both analyses. Twenty six QTLs were identified for the first time, with a single QTL ( qNN19a) in a 56 kb region explaining 32.56% of phenotypic variation, and an additional 10 of these were novel, stable QTLs. Moreover, 8 QTL hotpots on four different chromosomes were identified for the correlated traits.

          Conclusions

          With RAD-sequencing, some novel QTLs and important QTL clusters for both yield-related and quality traits were identified based on a new, high-density bin linkage map. Three predicted genes were selected as candidates that likely have a direct or indirect influence on both yield and quality in soybean. Our findings will be helpful for understanding common genetic control mechanisms of co-localized traits and to select cultivars for further analysis to predictably modulate soybean yield and quality simultaneously.

          Electronic supplementary material

          The online version of this article (doi:10.1186/s12864-017-3854-8) contains supplementary material, which is available to authorized users.

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          Control of grain size, shape and quality by OsSPL16 in rice.

          Shaokui Wang, Kun Wu, Qingbo Yuan … (2012)
          Grain size and shape are important components of grain yield and quality and have been under selection since cereals were first domesticated. Here, we show that a quantitative trait locus GW8 is synonymous with OsSPL16, which encodes a protein that is a positive regulator of cell proliferation. Higher expression of this gene promotes cell division and grain filling, with positive consequences for grain width and yield in rice. Conversely, a loss-of-function mutation in Basmati rice is associated with the formation of a more slender grain and better quality of appearance. The correlation between grain size and allelic variation at the GW8 locus suggests that mutations within the promoter region were likely selected in rice breeding programs. We also show that a marker-assisted strategy targeted at elite alleles of GS3 and OsSPL16 underlying grain size and shape can be effectively used to simultaneously improve grain quality and yield.
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            Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification.

            E Zietkiewicz, A. Rafalski, D Labuda (1994)
            Simple sequence repeats (SSR), or microsatellites, are ubiquitous in eukaryotic genomes. Here we demonstrate the utility of microsatellite-directed DNA fingerprinting by polymerase chain reaction (PCR) amplification of the interrepeat region. No sequencing is required to design the oligonucleotide primers. We tested primers anchored at 3' or 5' termini of the (CA)n repeats, extended into the flanking sequence by 2 to 4 nucleotide residues [3'-anchored primers: (CA)8RG, (CA)8RY, and (CA)7RTCY; and 5'-anchored primers: BDB(CA)7C, DBDA(CA)7, VHVG(TG)7 and HVH(TG)7T]. Radioactively labeled amplification products were analyzed by electrophoresis, revealing information on multiple genomic loci in a single gel lane. Complex, species-specific patterns were obtained from a variety of eukaryotic taxa. Intraspecies polymorphisms were also observed and shown to segregate as Mendelian markers. Inter-SSR PCR provides a novel fingerprinting approach applicable for taxonomic and phylogenetic comparisons and as a mapping tool in a wide range of organisms. This application of (CA)n repeats may be extended to different microsatellites and other common dispersed elements.
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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.
              Article 0 comments Cited 355 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Nianxi Liu: lnx69@126.com
                Mu Li: lm928094297@126.com
                Xiangbao Hu: 1584519512@qq.com
                Qibin Ma: maqibin@scau.edu.cn
                Yinghui Mu: youhymoon@scau.edu.cn
                Zhiyuan Tan: zytan@scau.edu.cn
                Qiuju Xia: xiaqiuju@genomics.cn
                Gengyun Zhang: zhanggengyun@genomics.cn
                Hai Nian:
                ORCID: http://orcid.org/0000-0003-0227-2045
                hnian@scau.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): 19 June 2017
                Publication date PMC-release: 19 June 2017
                Publication date Collection: 2017
                Volume: 18
                Electronic Location Identifier: 466
                Affiliations
                [1 ]ISNI 0000 0000 9546 5767, GRID grid.20561.30, The State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, , South China Agricultural University, ; Guangzhou, 510642 People’s Republic of China
                [2 ]ISNI 0000 0000 9546 5767, GRID grid.20561.30, The Key Laboratory of Plant Molecular Breeding, , South China Agricultural University, ; Guangzhou, 510642 People’s Republic of China
                [3 ]ISNI 0000 0000 9546 5767, GRID grid.20561.30, The Guangdong Subcenter of the National Center for Soybean Improvement, College of Agriculture, , South China Agricultural University, ; Guangzhou, 510642 People’s Republic of China
                [4 ]ISNI 0000 0000 9546 5767, GRID grid.20561.30, Joint Laboratory of Plant Breeding, , South China Agricultural University-ShanDong Shofine Seed Technology Co. Ltd, ; Guangzhou, 510642 People’s Republic of China
                [5 ]ISNI 0000 0001 2034 1839, GRID grid.21155.32, , Beijing Genome Institute (BGI), ; Shenzhen, 518083 People’s Republic of China
                Author information
                http://orcid.org/0000-0003-0227-2045
                Article
                Publisher ID: 3854
                DOI: 10.1186/s12864-017-3854-8
                PMC ID: 5477377
                PubMed ID: 28629322
                SO-VID: af24bff2-1042-4879-bb9b-69cf88a6a6df
                Copyright © © The Author(s). 2017
                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 : 3 March 2017
                Date accepted : 9 June 2017
                Funding
                Funded by: China Agricultural Research System
                Award ID: CARS-04-PS09
                Award Recipient :
                Funded by: Major Projects of New Varieties Cultivation of Genetically Modified Organisms
                Award ID: 2014ZX08004-002
                Award Recipient :
                Categories
                Subject: Research Article
                Custom metadata
                issue-copyright-statement © The Author(s) 2017

                ScienceOpen disciplines: Genetics
                Keywords: qtl,yield-related traits,quality traits,rad-sequencing,soybean
                Data availability:
                ScienceOpen disciplines: Genetics
                Keywords: qtl, yield-related traits, quality traits, rad-sequencing, soybean

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