QTL identification for seed weight and size based on a high-density SLAF-seq genetic map in peanut ( Arachis hypogaea  L.)

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Abstract

Background

The cultivated peanut is an important oil and cash crop grown worldwide. To meet the growing demand for peanut production each year, genetic studies and enhanced selection efficiency are essential, including linkage mapping, genome-wide association study, bulked-segregant analysis and marker-assisted selection. Specific locus amplified fragment sequencing (SLAF-seq) is a powerful tool for high density genetic map (HDGM) construction and quantitative trait loci (QTLs) mapping. In this study, a HDGM was constructed using SLAF-seq leading to identification of QTL for seed weight and size in peanut.

Results

A recombinant inbred line (RIL) population was advanced from a cross between a cultivar ‘Huayu36’ and a germplasm line ‘6–13’ with contrasting seed weight, size and shape. Based on the cultivated peanut genome, a HDGM was constructed with 3866 loci consisting of SLAF-seq and simple sequence repeat (SSR) markers distributed on 20 linkage groups (LGs) covering a total map distance of 1266.87 cM. Phenotypic data of four seed related traits were obtained in four environments, which mostly displayed normal distribution with varied levels of correlation. A total of 27 QTLs for 100 seed weight (100SW), seed length (SL), seed width (SW) and length to width ratio (L/W) were identified on 8 chromosomes, with LOD values of 3.16–31.55 and explaining phenotypic variance (PVE) from 0.74 to 83.23%. Two stable QTL regions were identified on chromosomes 2 and 16, and gene content within these regions provided valuable information for further functional analysis of yield component traits.

Conclusions

This study represents a new HDGM based on the cultivated peanut genome using SLAF-seq and SSRs. QTL mapping of four seed related traits revealed two stable QTL regions on chromosomes 2 and 16, which not only facilitate fine mapping and cloning these genes, but also provide opportunity for molecular breeding of new peanut cultivars with improved seed weight and size.

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Gene Ontology: tool for the unification of biology

Michael Ashburner, Catherine A. Ball, Judith Blake … (2002)

Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.

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SLAF-seq: An Efficient Method of Large-Scale De Novo SNP Discovery and Genotyping Using High-Throughput Sequencing

Xiaowen Sun, Dongyuan Liu, Xiaofeng Zhang … (2013)

Large-scale genotyping plays an important role in genetic association studies. It has provided new opportunities for gene discovery, especially when combined with high-throughput sequencing technologies. Here, we report an efficient solution for large-scale genotyping. We call it specific-locus amplified fragment sequencing (SLAF-seq). SLAF-seq technology has several distinguishing characteristics: i) deep sequencing to ensure genotyping accuracy; ii) reduced representation strategy to reduce sequencing costs; iii) pre-designed reduced representation scheme to optimize marker efficiency; and iv) double barcode system for large populations. In this study, we tested the efficiency of SLAF-seq on rice and soybean data. Both sets of results showed strong consistency between predicted and practical SLAFs and considerable genotyping accuracy. We also report the highest density genetic map yet created for any organism without a reference genome sequence, common carp in this case, using SLAF-seq data. We detected 50,530 high-quality SLAFs with 13,291 SNPs genotyped in 211 individual carp. The genetic map contained 5,885 markers with 0.68 cM intervals on average. A comparative genomics study between common carp genetic map and zebrafish genome sequence map showed high-quality SLAF-seq genotyping results. SLAF-seq provides a high-resolution strategy for large-scale genotyping and can be generally applicable to various species and populations.

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Natural variation in GS5 plays an important role in regulating grain size and yield in rice.

Yibo Li, Chuchuan Fan, Yongzhong Xing … (2011)

Increasing crop yield is one of the most important goals of plant science research. Grain size is a major determinant of grain yield in cereals and is a target trait for both domestication and artificial breeding(1). We showed that the quantitative trait locus (QTL) GS5 in rice controls grain size by regulating grain width, filling and weight. GS5 encodes a putative serine carboxypeptidase and functions as a positive regulator of grain size, such that higher expression of GS5 is correlated with larger grain size. Sequencing of the promoter region in 51 rice accessions from a wide geographic range identified three haplotypes that seem to be associated with grain width. The results suggest that natural variation in GS5 contributes to grain size diversity in rice and may be useful in improving yield in rice and, potentially, other crops(2).

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Author and article information

Contributors

Jing Chen: mianbaohua2008@126.com

Journal

Journal ID (nlm-ta): BMC Plant Biol

Journal ID (iso-abbrev): BMC Plant Biol

Title: BMC Plant Biology

Publisher: BioMed Central (London )

ISSN (Electronic): 1471-2229

Publication date (Electronic): 3 December 2019

Publication date PMC-release: 3 December 2019

Publication date Collection: 2019

Volume: 19

Electronic Location Identifier: 537

Affiliations

[1 ]ISNI 0000 0004 0644 6150, GRID grid.452757.6, Shandong Peanut Research Institute, ; Qingdao, 266100 People’s Republic of China

[2 ]ISNI 0000 0004 1936 738X, GRID grid.213876.9, Department of Horticulture, , University of Georgia Tifton Campus, ; Tifton, GA 31793 USA

[3 ]ISNI 0000 0000 9750 7019, GRID grid.27871.3b, State Key Laboratory for Crop Genetics and Germplasm Enhancement, , Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, ; Nanjing, 210095 People’s Republic of China

[4 ]ISNI 0000 0001 0017 5204, GRID grid.454840.9, Institute of Industrial Crops, , Jiangsu Academy of Agricultural Sciences, ; Nanjing, 210014 People’s Republic of China

[5 ]Qingdao Agricultural Radio and Television School, Qingdao, 266071 People’s Republic of China

Article

Publisher ID: 2164

DOI: 10.1186/s12870-019-2164-5

PMC ID: 6892246

PubMed ID: 31795931

SO-VID: ddc985f3-8bb9-4cc8-8320-ec5d5f6dde46

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 : 13 August 2019

Date accepted : 26 November 2019

Funding

Funded by: Visiting Scholar Project of Shandong Academy of Agricultural Sciences

Award ID: 2015-2016

Award Recipient : Jing Chen

Funded by: the Breeding Project from Department Science & Technology of Shandong Province

Award ID: 2017LNZ033, 2017LZGC003

Award Recipient : Jing Chen

Funded by: the Achievements Programs of Shandong Academy of Agricultural Sciences

Award ID: 2015CGPY03

Award Recipient : Jing Chen

Funded by: the Agricultural Scientific and the Technological Innovation Project of Shandong Academy of Agricultural Sciences

Award ID: CXGC2016B02, CXGC2018E21

Award Recipient : Jing Chen

Funded by: Qingdao People’s Livelihood Science and the Technology Project

Award ID: 19-6-1-61-nsh

Award Recipient : Jing Chen

Custom metadata

ScienceOpen disciplines: Plant science & Botany

Keywords: peanut,slaf-seq,high density genetic map,qtl,seed weight,seed size

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ScienceOpen disciplines: Plant science & Botany

Keywords: peanut, slaf-seq, high density genetic map, qtl, seed weight, seed size

QTL identification for seed weight and size based on a high-density SLAF-seq genetic map in peanut ( Arachis hypogaea L.)

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Abstract

Background

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Conclusions

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Plant MYBs

Most cited references 53

Gene Ontology: tool for the unification of biology

SLAF-seq: An Efficient Method of Large-Scale De Novo SNP Discovery and Genotyping Using High-Throughput Sequencing

Natural variation in GS5 plays an important role in regulating grain size and yield in rice.

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