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Genome-wide association study and genomic selection for soybean chlorophyll content associated with soybean cyst nematode tolerance

文献类型： 外文期刊

作者： Ravelombola, Waltram Second 1 ; Qin, Jun 1 ; Shi, Ainong 1 ; Nice, Liana 3 ; Bao, Yong 3 ; Lorenz, Aaron 3 ; Orf, Jame 1 ;

作者机构： 1.Univ Arkansas, Dept Hort, PTSC316, Fayetteville, AR 72701 USA

2.Hebei Acad Agr & Forestry Sci, Hebei Cereal & Oil Crop Inst, Shijiazhuang 050031, Hebei, Peoples R China

3.Univ Minnesota, Southern Res & Outreach Ctr, Waseca, MN 56093 USA

4.Univ Minnesota, Dept Agron & Plant Genet, St Paul, MN 55108 USA

5.Univ Minnesota, Dept Plant Pathol, St Paul, MN 55108 USA

关键词： Genome-wide association study (GWAS); Soybean cyst nematode (SCN); Leaf chlorophyll content; Single nucleotide polymorphism (SNP); Genomic selection (GS)

期刊名称：BMC GENOMICS （ 影响因子：3.969； 五年影响因子：4.478 ）

ISSN： 1471-2164

年卷期： 2019 年 20 卷 1 期

页码：

收录情况： SCI

摘要： Background Soybean cyst nematode (SCN), Heterodera glycines Ichinohe, has been one of the most devastating pathogens affecting soybean production. In the United States alone, SCN damage accounted for more than $1 billion loss annually. With a narrow genetic background of the currently available SCN-resistant commercial cultivars, high risk of resistance breakdown can occur. The objectives of this study were to conduct a genome-wide association study (GWAS) to identify QTL, SNP markers, and candidate genes associated with soybean leaf chlorophyll content tolerance to SCN infection, and to carry out a genomic selection (GS) study for the chlorophyll content tolerance. Results A total of 172 soybean genotypes were evaluated for the effect of SCN HG Type 1.2.3.5.6.7 (race 4) on soybean leaf chlorophyll. The soybean lines were genotyped using a total of 4089 filtered and high-quality SNPs. Results showed that (1) a large variation in SCN tolerance based on leaf chlorophyll content indices (CCI); (2) a total of 22, 14, and 16 SNPs associated with CCI of non-SCN-infected plants, SCN-infected plants, and reduction of CCI SCN, respectively; (3) a new locus of chlorophyll content tolerance to SCN mapped on chromosome 3; (4) candidate genes encoding for Leucine-rich repeat protein, plant hormone signaling molecules, and biomolecule transporters; and (5) an average GS accuracy ranging from 0.31 to 0.46 with all SNPs and varying from 0.55 to 0.76 when GWAS-derived SNP markers were used across five models. This study demonstrated the potential of using genome-wide selection to breed chlorophyll-content-tolerant soybean for managing SCN. Conclusions In this study, soybean accessions with higher CCI under SCN infestation, and molecular markers associated with chlorophyll content related to SCN were identified. In addition, a total of 15 candidate genes associated with chlorophyll content tolerance to SCN in soybean were also identified. These candidate genes will lead to a better understanding of the molecular mechanisms that control chlorophyll content tolerance to SCN in soybean. Genomic selection analysis of chlorophyll content tolerance to SCN showed that using significant SNPs obtained from GWAS could provide better GS accuracy.

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