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. 2019 Nov 27;20(1):904.
doi: 10.1186/s12864-019-6275-z.

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

Waltram Second Ravelombola  1 , Jun Qin  1   2 , Ainong Shi  3 , Liana Nice  4   5 , Yong Bao  4   5 , Aaron Lorenz  4   5 , James H Orf  4   5 , Nevin D Young  6 , Senyu Chen  7   8
Affiliations

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

Waltram Second Ravelombola et al. BMC Genomics. .

Abstract

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.

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

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Combined violin-boxplots representing the probability density function of leaf chlorophyll content indices for plants grown in SCN-infested soils (yellow), plants grown in soils without SCN (green), and percentage reduction in leaf chlorophyll content indices due to SCN
Fig. 2
Fig. 2
Graphs showing Manhattan plots and QQ-plots for leaf chlorophyll content indices (CCI) of plants non-infected by SCN, CCI plants infected by SCN, and reduction in CCI by SCN. a Manhattan plot for CCI of plants without SCN, b QQ-plot for CCI of the non-infected plants, c Manhattan plot for CCI of the SCN-infected plants, d QQ-plot for CCI of the SCN-infected plants, e Manhattan plot for reduction in CCI by SCN, and (f): QQ-plot for reduction in CCI
Fig. 3
Fig. 3
Genomic selection accuracy under 5 GS models for leaf chlorophyll content indices for plants without SCN infection
Fig. 4
Fig. 4
Genomic selection accuracy under 5 GS models for leaf chlorophyll content indices of the SCN-infected plants
Fig. 5
Fig. 5
Genomic selection accuracy under 5 GS models for reduction in leaf chlorophyll content indices by SCN
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