Dataset Information

Combining QTL-seq and linkage mapping to fine map a wild soybean allele characteristic of greater plant height.

ABSTRACT: BACKGROUND:Plant height (PH) is an important agronomic trait and is closely related to yield in soybean [Glycine max (L.) Merr.]. Previous studies have identified many QTLs for PH. Due to the complex genetic background of PH in soybean, there are few reports on its fine mapping. RESULTS:In this study, we used a mapping population derived from a cross between a chromosome segment substitution line CSSL3228 (donor N24852 (G. Soja), a receptor NN1138-2 (G. max)) and NN1138-2 to fine map a wild soybean allele of greater PH by QTL-seq and linkage mapping. We identified a QTL for PH in a 1.73 Mb region on soybean chromosome 13 through QTL-seq, which was confirmed by SSR marker-based classical QTL mapping in the mapping population. The linkage analysis showed that the QTLs of PH were located between the SSR markers BARCSOYSSR_13_1417 and BARCSOYSSR_13_1421 on chromosome 13, and the physical distance was 69.3 kb. RT-PCR and sequence analysis of possible candidate genes showed that Glyma.13 g249400 revealed significantly higher expression in higher PH genotypes, and the gene existed 6 differences in the amino acids encoding between the two parents. CONCLUSIONS:Data presented here provide support for Glyma.13 g249400 as a possible candidate genes for higher PH in wild soybean line N24852.

SUBMITTER: Zhang X

PROVIDER: S-EPMC5870336 | biostudies-literature | 2018 Mar

REPOSITORIES: biostudies-literature

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Combining QTL-seq and linkage mapping to fine map a wild soybean allele characteristic of greater plant height.

Zhang Xiaoli X Wang Wubin W Guo Na N Zhang Youyi Y Bu Yuanpeng Y Zhao Jinming J Xing Han H

BMC genomics 20180327 1

<h4>Background</h4>Plant height (PH) is an important agronomic trait and is closely related to yield in soybean [Glycine max (L.) Merr.]. Previous studies have identified many QTLs for PH. Due to the complex genetic background of PH in soybean, there are few reports on its fine mapping.<h4>Results</h4>In this study, we used a mapping population derived from a cross between a chromosome segment substitution line CSSL3228 (donor N24852 (G. Soja), a receptor NN1138-2 (G. max)) and NN1138-2 to fine ...[more]

PMID: 29587637

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Project description:BackgroundGenomic analysis technologies can promote efficient fruit tree breeding. Genotyping by sequencing (GBS) enables generating efficient data for high-quality genetic map construction and QTL analysis in a relatively accessible way. Furthermore, High-resolution genetic map construction and accurate QTL detection can significantly narrow down the putative candidate genes associated with important plant traits.ResultsWe genotyped 162 offspring in the F1 'Spadona' x 'Harrow Sweet' pear population using GBS. An additional 21 pear accessions, including the F1 population's parents, from our germplasm collection were subjected to GBS to examine diverse genetic backgrounds that are associated to agriculturally relevant traits and to enhance the power of SNP calling. A standard SNP calling pipeline identified 206,971 SNPs with Asian pear ('Suli') as the reference genome and 148,622 SNPs with the European genome ('Bartlett'). These results enabled constructing a genetic map, after further stringent SNP filtering, consisting of 2036 markers on 17 linkage groups with a length of 1433 cM and an average marker interval of 0.7 cM. We aligned 1030 scaffolds covering a total size of 165.5 Mbp (29%) of the European pear genome to the 17 linkage groups. For high-resolution QTL analysis covering the whole genome, we used phenotyping for vegetative budbreak time in the F1 population. New QTLs associated to vegetative budbreak time were detected on linkage groups 5, 13 and 15. A major QTL on linkage group 8 and an additional QTL on linkage group 9 were confirmed. Due to the significant genotype-by-environment (GxE) effect, we were able to identify novel interaction QTLs on linkage groups 5, 8, 9 and 17. Phenotype-genotype association analysis in the pear accessions for main genotype effect was conducted to support the QTLs detected in the F1 population. Significant markers were detected on every linkage group to which main genotype effect QTLs were mapped.ConclusionsThis is the first vegetative budbreak study of European pear that makes use of high-resolution genetic mapping. These results provide tools for marker-assisted selection and accurate QTL analysis in pear, and specifically at vegetative budbreak, considering the significant GxE and phenotype-plasticity effects.

Dataset Information

Combining QTL-seq and linkage mapping to fine map a wild soybean allele characteristic of greater plant height.

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Combining QTL-seq and linkage mapping to fine map a wild soybean allele characteristic of greater plant height.

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