Genetic diversity and population structure analyses and genome-wide association studies of photoperiod sensitivity in cotton (Gossypium hirsutum L.)

S Anjan Gowda; Fred M Bourland; Baljinder Kaur; Don C Jones; Vasu Kuraparthy

doi:10.1007/s00122-023-04477-w

Genetic diversity and population structure analyses and genome-wide association studies of photoperiod sensitivity in cotton (Gossypium hirsutum L.)

Theor Appl Genet. 2023 Oct 24;136(11):230. doi: 10.1007/s00122-023-04477-w.

Authors

S Anjan Gowda¹, Fred M Bourland², Baljinder Kaur¹, Don C Jones³, Vasu Kuraparthy⁴

Affiliations

¹ Crop and Soil Sciences Department, North Carolina State University, Raleigh, NC, 27695, USA.
² NE Research and Extension Center, Crop, Soil, and Environmental Sciences, University of Arkansas, Keiser, AR, 72351, USA.
³ Cotton Incorporated, 6399 Weston Parkway, Cary, NC, 27513, USA.
⁴ Crop and Soil Sciences Department, North Carolina State University, Raleigh, NC, 27695, USA. vasu_kuraparthy@ncsu.edu.

PMID: 37875695
DOI: 10.1007/s00122-023-04477-w

Abstract

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 (F_ST) of 0.65 was found between landrace accessions of Guatemala and the Plains-type cultivars from Southwest cotton region while the lowest F_ST 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.

MeSH terms

Cotton Fiber
Genome-Wide Association Study*
Gossypium* / genetics
Photoperiod
Plant Breeding
Polymorphism, Single Nucleotide