Fine-mapping and identifying candidate genes conferring resistance to Soybean mosaic virus strain SC20 in soybean

Abstract

The Mendelian gene conferring resistance to Soybean mosaic virus Strain SC20 in soybean was fine-mapped onto a 79-kb segment on Chr.13 where two closely linked candidate genes were identified and qRT-PCR verified. Soybean mosaic virus (SMV) threatens the world soybean production, particularly in China. A country-wide SMV strain system composed of 22 strains was established in China, among which SC20 is a dominant strain in five provinces in Southern China. Resistance to SC20 was evaluated in parents, F, F and the F RIL (recombinant inbred line) population derived from a cross between Qihuang-1 (resistant) and NN1138-2 (susceptible). The segregation ratio of resistant to susceptible in the populations suggested a single dominant gene involved in the resistance to SC20 in Qihuang-1. A "partial genome mapping strategy" was used to map the resistance gene on Chromosome 13. Linkage analysis between 178 RILs and genetic markers showed that the SC20-resistance gene located at 3.9 and 3.8 cM to the flanking markers BARCSOYSSR_13_1099 and BARCSOYSSR_13_1185 on Chromosome 13. Subsequently, a residual heterozygote segregating population with 346 individuals was developed by selfing four plants heterozygous at markers adjacent to the tentative SC20-resistance gene; then, the candidate region was delimited to a genomic interval of approximately 79 kb flanked by the new markers gm-ssr_13-14 and gm-indel_13-3. Among the seven annotated candidate genes in this region, two genes, Glyma.13G194700 and Glyma.13G195100, encoding Toll Interleukin Receptor-nucleotide-binding-leucine-rich repeat resistance proteins were identified as candidate resistance genes by quantitative real-time polymerase chain reaction and sequence analysis. The two closely linked genes work together to cause the phenotypic segregation as a single Mendelian gene. These results will facilitate marker-assisted selection, gene cloning and breeding for the resistance to SC20.

Fine mapping and identification of the fuzzless gene GaFzl in DPL972 (Gossypium arboreum)

“…Identification of target genes based on natural or mutagenic mutants is the central idea of forward genetics (Chang et al 2016; Andres et al 2017; Liu et al 2018; Qureshi et al 2018; Yang et al 2018). Map-based cloning, the most efficient and visual strategy for gene identification, has been used to obtain numerous genes (Dou et al 2018; Han et al 2018; Jeong et al 2018; Karthikeyan et al 2018). For instance, a previous study used this technique to map and characterize a dominant single gene Gl 2 e that controls the development of gland pigment (Cheng et al 2016).…”

Impacts of genomic research on soybean improvement in East Asia

“…Among them, SC20 is the most widespread in the five provinces in southern China, affecting soybean cultivation in that region. A SMV resistance QTL was finemapped to a 79-kb region on chromosome 13 of Qihuang-1, flanked by a new SSR marker and a new INDEL marker (Table 2) (Karthikeyan et al 2018). Two TIR-NB-LRR protein-encoding genes that are highly polymorphic between the two parents in the mapping population are identified within this QTL, and they are highly likely to be the candidates of the SC20 resistance gene (Karthikeyan et al 2018).…”

Genome-Wide Association Study for Resistance to the <em>Meloidogyne javanica</em> Causing Root-Knot Nematode in Soybean

“…Recently, by the fine-mapping of a locus conferring resistance to Soybean Mosaic Virus (SMV) identified a region of 79 kbp on chromosome 13 [54], and among the genes located in the region, it was identified the Glyma13g.194700, which had high gene expression levels at 8 hpi (hours post inoculation) [55]. Locus conferring both resistance to nematode and virus was already described.…”