Abstract
BackgroundSoybean 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.ResultsA 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.ConclusionsIn 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.
Highlights
Soybean cyst nematode (SCN), Heterodera glycines Ichinohe, has been one of the most devastating pathogens affecting soybean production
The objectives of this study were (i) to conduct a genome-wide association study to identify QTL associated with leaf chlorophyll content in soybean in SCN infested and non-infested soils, and the QTL associated with reduction of chlorophyll content by SCN; (ii) identify Single nucleotide polymorphism (SNP) markers and candidate genes associated with the traits; (iii) to carry out a genomic selection study for tolerance of soybean chlorophyll content to SCN infection
Chlorophyll content phenotyping associated with SCN Soybean leaf chlorophyll content (CCI) in non-SCNinfestation recorded at 8 weeks after planting was significantly different among the genotypes (F-value = 11.17, pvalue< 0.0001) (Table 1)
Summary
Soybean cyst nematode (SCN), Heterodera glycines Ichinohe, has been one of the most devastating pathogens affecting soybean production. Soybean cyst nematode (SCN), Heterodera glycines Ichinohe, is an important pest with total annual yield losses about $1.5 billion in the U.S alone [1]. Iron-deficiency chlorosis (IDC) of soybean, in particular, is common in the North Central region, the major soybean production region in the USA. It occurs in high pH soil, but many biotic and abiotic factors affect its occurrence [5,6,7,8]. Managing SCN and nutritional deficiencies is important for soybean productivity in many fields in the North Central USA and some other regions in the world
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