GWAS Mediated Elucidation of Heterosis for Metric Traits in Cotton (Gossypium hirsutum L.) Across Multiple Environments

Abstract

For about a century, plant breeding has widely exploited the heterosis phenomenon–often considered as hybrid vigor–to increase agricultural productivity. The ensuing F1 hybrids can substantially outperform their progenitors due to heterozygous combinations that mitigate deleterious mutations occurring in each genome. However, only fragmented knowledge is available concerning the underlying genes and processes that foster heterosis. Although cotton is among the highly valued crops, its improvement programs that involve the exploitation of heterosis are still limited in terms of significant accomplishments to make it broadly applicable in different agro-ecological zones. Here, F1 hybrids were derived from mating a diverse Upland Cotton germplasm with commercially valuable cultivars in the Line × Tester fashion and evaluated across multiple environments for 10 measurable traits. These traits were dissected into five different heterosis types and specific combining ability (SCA). Subsequent genome-wide predictions along-with association analyses uncovered a set of 298 highly significant key single nucleotide polymorphisms (SNPs)/Quantitative Trait Nucleotides (QTNs) and 271 heterotic Quantitative Trait Nucleotides (hQTNs) related to agronomic and fiber quality traits. The integration of a genome wide association study with RNA-sequence analysis yielded 275 candidate genes in the vicinity of key SNPs/QTNs. Fiber micronaire (MIC) and lint percentage (LP) had the maximum number of associated genes, i.e., each with 45 related to QTNs/hQTNs. A total of 54 putative candidate genes were identified in association with HETEROSIS of quoted traits. The novel players in the heterosis mechanism highlighted in this study may prove to be scientifically and biologically important for cotton biologists, and for those breeders engaged in cotton fiber and yield improvement programs.

Inheritance, QTLs, and Candidate Genes of Lint Percentage in Upland Cotton

“…The correlations between GD and F 1 performance, mid-parent heterosis (MPH), and best parent heterosis (BPH) are significant for LP ( Geng et al, 2021 ). Fourteen putative candidate genes were identified as associated with heterosis of LP ( Sarfraz et al, 2021 ). A study with CP-15/2, NIAB Krishma, CIM-482, MS-39, and S-12 found greater specific combining ability (SCA) variance than general combining ability (GCA) variance for LP (0.470), indicating the predominance of non-additive genes ( Imran et al, 2012 ).…”

“…Fine mapping of the major effective QTLs for LP makes it possible to clone the candidate genes by map-based cloning. The availability of whole-genome sequences also paves a way to identify and clone functional genes, e.g., those relating to fiber development and increased LP ( Pan et al, 2020 ; Sarfraz et al, 2021 ).…”

Genetic Diversity, QTL Mapping, and Marker-Assisted Selection Technology in Cotton (Gossypium spp.)

“…At these loci, they found 14 genes with non-synonymous SNPs. Sarfraz et al (2021) have conducted subsequent genome-wide predictions along with association analyses that uncovered a set of highly significant key SNPs related to agronomic and fiber quality traits ( Sarfraz et al, 2021 ). The integration of a GWAS with RNA-sequence analysis yielded 275 candidate genes near the key SNPs.…”

Transcriptome and Metabolome Analyses of Salt Stress Response in Cotton (Gossypium hirsutum) Seed Pretreated with NaCl

“…Understanding the response of the cotton crop to salt, its tolerance mechanism, and comprehensive knowledge related to management practices may be helpful [1,17]. Recently, many advanced studies, such as whole-genome sequencing, on different cotton species (diploid and tetraploid) facilitated us with the reference genome(s) of cotton for a better understanding of genes and transcription factors in relation to their functions under stress conditions in terms of controlling several biological and metabolic pathways [2,6,14,[16][17][18][19][20].…”