RESUMEN
KEY MESSAGE: A GWAS in an elite diversity panel, evaluated across 10 environments, identified genomic regions regulating six fiber quality traits, facilitating genomics-assisted breeding and gene discovery in upland cotton. In this study, an elite diversity panel of 348 upland cotton accessions was evaluated in 10 environments across the US Cotton Belt and genotyped with the cottonSNP63K array, for a genome-wide association study of six fiber quality traits. All fiber quality traits, upper half mean length (UHML: mm), fiber strength (FS: g tex-1), fiber uniformity (FU: %), fiber elongation (FE: %), micronaire (MIC) and short fiber content (SFC: %), showed high broad-sense heritability (> 60%). All traits except FE showed high genomic heritability. UHML, FS and FU were all positively correlated with each other and negatively correlated with FE, MIC and SFC. GWAS of these six traits identified 380 significant marker-trait associations (MTAs) including 143 MTAs on 30 genomic regions. These 30 genomic regions included MTAs identified in at least three environments, and 23 of them were novel associations. Phenotypic variation explained for the MTAs in these 30 genomic regions ranged from 6.68 to 11.42%. Most of the fiber quality-associated genomic regions were mapped in the D-subgenome. Further, this study confirmed the pleiotropic region on chromosome D11 (UHML, FS and FU) and identified novel co-localized regions on D04 (FU, SFC), D05 (UHML, FU, and D06 UHML, FU). Marker haplotype analysis identified superior combinations of fiber quality-associated genomic regions with high trait values (UHML = 32.34 mm; FS = 32.73 g tex-1; FE = 6.75%). Genomic analyses of traits, haplotype combinations and candidate gene information described in the current study could help leverage genetic diversity for targeted genetic improvement and gene discovery for fiber quality traits in cotton.
Asunto(s)
Fibra de Algodón , Genotipo , Gossypium , Fenotipo , Sitios de Carácter Cuantitativo , Gossypium/genética , Gossypium/crecimiento & desarrollo , Fibra de Algodón/análisis , Polimorfismo de Nucleótido Simple , Estudio de Asociación del Genoma Completo , Estudios de Asociación Genética , Desequilibrio de Ligamiento , Mapeo Cromosómico/métodos , Genoma de Planta , FitomejoramientoRESUMEN
KEY MESSAGE: Genetic diversity and population structure analyses showed progressively narrowed diversity in US Upland cotton compared to land races. GWAS identified genomic regions and candidate genes for photoperiod sensitivity in cotton. Six hundred fifty-seven accessions that included elite cotton germplasm (DIV panel), lines of a public cotton breeding program (FB panel), and tropical landrace accessions (TLA panel) of Gossypium hirsutum L. were genotyped with cottonSNP63K array and phenotyped for photoperiod sensitivity under long day-length conditions. The genetic diversity analysis using 26,952 polymorphic SNPs indicated a progressively narrowed diversity from the landraces (0.230) to the DIV panel accessions (0.195) and FB panel (0.116). Structure analysis in the US germplasm identified seven subpopulations representing all four major regions of the US cotton belt. Three subpopulations were identified within the landrace accessions. The highest fixation index (FST) of 0.65 was found between landrace accessions of Guatemala and the Plains-type cultivars from Southwest cotton region while the lowest FST values were between the germplasms of Mid-South and Southeastern regions. Genome wide association studies (GWAS) of photoperiod response using 600 phenotyped accessions identified 14 marker trait associations spread across eight Upland cotton chromosomes. Six of these marker trait associations, on four chromosomes (A10, D04, D05, and D06), showed significant epistatic interactions. Targeted genomic analysis identified regions with 19 candidate genes including Transcription factor Vascular Plant One-Zinc Finger 1 (VOZ1) and Protein Photoperiod-Independent Early Flowering 1 (PIE1) genes. Genetic diversity and genome wide analyses of photoperiod sensitivity in diverse cotton germplasms will enable the use of genomic tools to systematically utilize the tropical germplasm and its beneficial alleles for broadening the genetic base in Upland cotton.
Asunto(s)
Estudio de Asociación del Genoma Completo , Gossypium , Gossypium/genética , Fotoperiodo , Fitomejoramiento , Polimorfismo de Nucleótido Simple , Fibra de AlgodónRESUMEN
KEY MESSAGE: Identification 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. Cotton bacterial leaf blight (CBB), caused by Xanthomonas citri subsp. malvacearum (Xcm), has periodically been a damaging disease in the USA. Identification and deployment of genetic resistance in cotton cultivars is the most economical and efficient means of reducing crop losses due to CBB. In the current study, genome-wide association study (GWAS) of CBB resistance using an elite diversity panel of 380 accessions, genotyped with the cotton single nucleotide polymorphism (SNP) 63 K array, and phenotyped with race-18 of CBB, localized the CBB resistance to a 2.01-Mb region in the long arm of chromosome D02. Molecular genetic mapping using an F6 recombinant inbred line (RIL) population showed the CBB resistance in cultivar Arkot 8102 was controlled by a single locus (BB-13). The BB-13 locus was mapped within the 0.95-cM interval near the telomeric region in the long arm of chromosome D02. Flanking SNP markers, i04890Gh and i04907Gh of the BB-13 locus, identified from the combined linkage analysis and GWAS, targeted it to a 371-Kb genomic region. Candidate gene analysis identified thirty putative gene sequences in the targeted genomic region. Nine of these putative genes and two NBS-LRR genes adjacent to the targeted region were putatively involved in plant disease resistance and are possible candidate genes for BB-13 locus. Genetic mapping and genomic targeting of the BB13 locus in the current study will help in cloning the CBB-resistant gene and establishing the molecular genetic architecture of the BB-13 locus towards developing durable resistance to CBB in cotton.
Asunto(s)
Estudio de Asociación del Genoma Completo , Gossypium , Polimorfismo de Nucleótido Simple , Mapeo Cromosómico , Genómica , Enfermedades de las Plantas/genética , Enfermedades de las Plantas/microbiologíaRESUMEN
Fibre quality improvement in Gossypium hirsutum is one of the long thought objectives for sustainability of cotton improvement. The efforts to transfer G. barbadense alleles in to G. hirsutum for enhanced fibre quality is still under process across the world. To meet the future fibre quality demand in India, here we report development of G. barbadense X G. barbadense recombinant inbred mapping population that has huge potential for precise mapping of extra-long staple traits. The two-location evaluation and variability analysis for extra-long staple traits such as fibre length (24.91 to 34.06 mm), fibre strength (25.02 to 35.86 g/tex), micronaire (2.89-4.57), uniformity index (64.08-98.83), fibre elongation (5.37-6.60) and maturity ratio (0.48-0.76) were highly satisfactory. The principal component analysis indicates that the principal component-1 explaining 23.12% variance had maximum values of Eigen vectors explained by fibre strength (-0.464), length (-0.469), elongation (-0.448), maturity ratio (0.312) and micronaire value (0.306) indicating the worth of the population for which it was developed. The correlation analysis indicated that the fibre length and strength could be simultaneously improved without any impact on seed cotton yield since both traits were positively associated with each other and also showed nonsignificant association with seed cotton yield. A total of 255 recombinant inbred lines (RILs) showed normal distribution from both Z-score of skewness/kurtosis analysis and quartile-quartile plots indicating that they can be readily utilized for genotyping with latest available technologies such as genotype-by-sequencing for effective mapping of extra-long staple traits in cotton.