Role of SNPs in determining QTLs for major traits in cotton

Abstract

A single nucleotide polymorphism is the simplest form of genetic variation among individuals and can induce minor changes in phenotypic, physiological and biochemical characteristics. This polymorphism induces various mutations that alter the sequence of a gene which can lead to observed changes in amino acids. Several assays have been developed for identification and validation of these markers. Each method has its own advantages and disadvantages but genotyping by sequencing is the most common and most widely used assay. These markers are also associated with several desirable traits like yield, fibre quality, boll size and genes respond to biotic and abiotic stresses in cotton. Changes in yield related traits are of interest to plant breeders. Numerous quantitative trait loci with novel functions have been identified in cotton by using these markers. This information can be used for crop improvement through molecular breeding approaches. In this review, we discuss the identification of these markers and their effects on gene function of economically important traits in cotton.

Genetic Basis of Fiber Improvement and Decreased Stress Tolerance in Cultivated Versus Semi-Domesticated Upland Cotton

“…The large number of wild Gossypium species presents an impressive range of variation in many characteristics, such as high fiber strength, disease resistance, nectariless, and glandless traits, all of which are potentially available for exploitation in cotton improvement programs (Wendel et al, 2009). Several stress-tolerance associated QTLs have been excavated in modern cultivated cotton, however, the excellent stress-tolerance loci still remain unknown in wild cotton (Majeed et al, 2019). Therefore, mining and restoring crop plant alleles from wild ancestors that were ‘‘left behind’’ during domestication may be useful for the improvement of productivity under stress conditions in modern cotton breeding.…”

Heat Stress in Cotton: A Review on Predicted and Unpredicted Growth-Yield Anomalies and Mitigating Breeding Strategies

“…Numerous markers such as amplified fragment length polymorphism (AFLP) and randomly amplified polymorphic DNA (RAPD) markers have been successfully utilized screening cotton genotypes for heat tolerance in the past [149,150]. Currently, simple sequence repeats (SSRs) and single nucleotide polymorphism (SNPs) are widely used markers for identifying quantitative traits loci (QTLs) related to stress tolerance in cotton [151,152]. The experiments were conducted by using heat tolerant and susceptible cultivars to determine heat responsive genes in upland cotton.…”

Revamping of Cotton Breeding Programs for Efficient Use of Genetic Resources under Changing Climate

“…Screening of domesticated and wild cotton germplasm for various agronomic traits drive the cotton breeding programs by hybridizing these attributes. Also, fine QTL mapping of these attributes associated with heat and drought stress tolerance can speed-up the hybridization process and decrease the linkage-drags in the advanced breeding lines [60,61]. As there were many other agronomically important genes found using forward and reverse genetic approaches.…”