Identification and genomic characterization of major effect bacterial blight resistance locus (BB-13) in Upland cotton (Gossypium hirsutum L.)

Abstract

Cotton bacterial leaf blight (CBB), caused by Xanthomonas citri subsp. malvacearum (Xcm) has been periodically a damaging disease in the U.S.A. Identi cation and deployment of genetic resistance in the cotton cultivars is the most economical and e cient means of reducing the crop losses due to CBB. In the current study, a combined genome-wide association study (GWAS) and linkage-mapping approach was used to map the CBB resistance gene in Upland cotton. An elite diversity panel of 380 accessions, genotyped with the Cotton 63K single nucleotide polymorphism (SNP) array and phenotyped with race-18 of CBB was used in the GWAS. The GWAS localized the CBB resistance to a 2.01 Mb region in the long arm of chromosome D02. Mapping of this CBB resistance was further resolved using linkage mapping in an F 6 recombinant inbred line (RIL) population derived from Acala Maxxa × Arkot 8102. The CBB resistance in Arkot 8102 showed monogenic inheritance. The CBB resistance locus (BB-13) was mapped within the 0.95 cM interval near the telomeric region in the long arm of chromosome D02. Flanking SNP markers, i25755Gh (p = 19.29) and i46775Gh (p = 19.29) of the BB-13 locus from the linkage analysis showed the highest signi cant marker-trait associations (MTAs) in the GWAS study. Using these SNPs, we targeted the BB-13 locus to a 371 Kb genomic region on chromosome D02. Candidate gene analysis identi ed thirty putative gene sequences in the targeted region. Nine of the thirty putative genes were involved in disease resistance in plants. Key MessageIdenti cation and genomic characterization of major resistance locus against cotton bacterial blight (CBB) using GWAS and linkage mapping to enable genomics-based development of durable CBB resistance and gene discovery in cotton.

Identification of quantitative trait loci for fiber quality, yield, and plant height traits in Upland cotton

“…Small mapping population size would result in lower genetic map resolution and might not have allowed us to detect all the possible minor QTL. However, our results from 110 RILs showed that all the chromosome linkage maps showed good marker coverage (∼96%) in comparison to the physical map, which is within the range of physical map coverage (92.50% to 97.99%) of the previously reported linkage maps (Gowda et al., 2022; Li et al., 2016; Tan et al., 2018). Further, our study using a population size of 110 RILs is sufficient to identify QTL with major effects (Xu, 2003) as well as detecting 16 QTL with minor effects.…”

“…Further, more markers were mapped to D subgenome (56.05%) than to A subgenome (43.95%) (Table 3), which could be attributed to relatively higher number SNPs of D subgenome represented in the CottonSNP63K array. This distribution of markers agrees with previous studies (Gowda et al, 2022;Hulse-Kemp et al, 2015b;Li et al, 2016;Ulloa et al, 2017;Zhang et al, 2019;Zhu et al,2021). The constructed linkage map in our study covered 96.05% of the Upland cotton genome, which falls under the range of 92.57%-98.8% as reported by Li et al (2016) andZhnag et al (2019) in Upland cotton intraspecific population.…”

“…At present, two SNP arrays are available in cotton, a 63K SNP array and an 80K SNP array (Cai et al., 2017; Hulse‐Kemp et al., 2015b). These SNP arrays have been used to assess genetic diversity (Billings et al., 2021), perform genome‐wide association studies (GWAS) (Cai et al., 2017; Gowda et al., 2022; Song et al., 2021; Sun et al., 2017), construct genetic maps (Hulse‐Kemp et al., 2015b; Zhang et al., 2019; Zhu et al., 2021), and detect QTL for fiber quality traits, yield traits, and morphological traits (Li et al., 2016; Zhang et al., 2019; Zhu et al., 2021). However, only a few studies have reported their use in identifying novel and stable QTL and develop functional markers for fiber quality traits, yield traits, and plant height in intraspecific Upland cotton populations.…”

Development and validation of Kompetitive allele‐specific PCR (KASP) markers for bacterial blight resistant locus BB‐13 in Upland cotton (Gossypium hirsutum L.)

“…The panel represents a major portion of genetic diversity present in US Upland cotton (Table S1). One hundred and four recombinant inbred lines (RILs) derived from Acala Maxxa (PI 540885; DIV 017) ✗ Arkot 8102 (PI 595852; DIV042) (Bourland et al., 1997) that were previously phenotyped for CBB response to race 18 were used to validate the KASP markers (Gowda et al., 2022). The KASP markers most closely linked and diagnostic for the BB‐13 locus were further used to validate its applicability and to test for the presence and segregation of the BB‐13 locus in an independent RIL population.…”

“…Forty‐five RILs along with two parental accessions were phenotyped for CBB response to race 18 of Xcm at the seedling stage in growth chambers as described by Gowda et al. (2022). The segregation ratios of phenotypes of the RIL population were calculated using a chi‐square analysis under the assumption that a single dominant gene controls the CBB resistance.…”