Quantitative Trait Locus Analysis and Identification of Candidate Genes Affecting Seed Size and Shape in an Interspecific Backcross Inbred Line Population of Gossypium hirsutum × Gossypium barbadense

Abstract

Seed size and shape are key agronomic traits affecting seedcotton yield and seed quality in cotton (Gossypium spp.). However, the genetic mechanisms that regulate the seed physical traits in cotton are largely unknown. In this study, an interspecific backcross inbred line (BIL) population of 250 BC1F7 lines, derived from the recurrent parent Upland CRI36 (Gossypium hirsutum) and Hai7124 (Gossypium barbadense), was used to investigate the genetic basis of cotton seed physical traits via quantitative trait locus (QTL) mapping and candidate gene identification. The BILs were tested in five environments, measuring eight seed size and shape-related traits, including 100-kernel weight, kernel length width and their ratio, kernel area, kernel girth, kernel diameter, and kernel roundness. Based on 7,709 single nucleotide polymorphic (SNP) markers, a total of 49 QTLs were detected and each explained 2.91–35.01% of the phenotypic variation, including nine stable QTLs mapped in at least three environments. Based on pathway enrichment, gene annotation, genome sequence, and expression analysis, five genes encoding starch synthase 4, transcription factor PIF7 and MYC4, ubiquitin-conjugating enzyme E27, and THO complex subunit 4A were identified as candidate genes that might be associated with seed size and shape. Our research provides valuable information to improve seed physical traits in cotton breeding.

Research on the evolutionary history of the morphological structure of cotton seeds: a new perspective based on high-resolution micro-CT technology

“…(2022) analyzed the correlations of seed traits including weight of 100 seeds, seed length, seed width, seed length-width ratio, seed area, seed perimeter, seed diameter, and sphericity with an automatic seed testing machine and found that these morphological traits are environmentally stable. In the correlation analysis conducted by Wu et al. (2022) , the correlation between seed length and seed width was low, while the correlation between the seed width and seed thickness was high, which was consistent with our research results.…”

“… Wu et al. (2022) analyzed the correlations of seed traits including weight of 100 seeds, seed length, seed width, seed length-width ratio, seed area, seed perimeter, seed diameter, and sphericity with an automatic seed testing machine and found that these morphological traits are environmentally stable.…”

“…The seed’s morphological structure is closely associated with its functions, and differences exist in seed functions based on their various morphological structures. The size and shape of seeds are key agronomical traits that influence cotton yield and quality ( Wu et al., 2022 ). Larger and fuller seeds demonstrate superior early growth, uniformity, and higher metrics such as single plant dry matter weight, root-to-shoot ratio, emergence rate, and leaf area ( Liu et al., 1997 ; Wang et al., 2008 ).…”