Abstract
Cotton production is on the decline due to ever-changing environmental conditions. Drought and salinity stress contribute to over 30% of total loss in cotton production, the situation has worsened more due to the narrow genetic base of the cultivated upland cotton. The genetic diversity of upland cotton has been eroded over the years due to intense selection and inbreeding. To break the bottleneck, the wild cotton progenitors offer unique traits which can be introgressed into the cultivated cotton, thereby improving their performance. In this research, we developed a BC2F2 population between wild male parent, G. tomentosum as the donor, known for its high tolerance to drought and the elite female parent, G. hirsutum as the recurrent parent, which is high yielding but sensitive to drought stress. The population was genotyped through the genotyping by sequencing (GBS) method, in which 10,888 single-nucleotide polymorphism (SNP) s were generated and used to construct a genetic map. The map spanned 4191.3 cM, with average marker distance of 0.3849 cM. The map size of the two sub genomes had a narrow range, 2149 cM and 2042.3 cM for At and Dt_sub genomes respectively. A total of 66,434 genes were mined, with 32,032 (48.2%) and 34,402 (51.8%) genes being obtained within the At and Dt_sub genomes respectively. Pkinase (PF00069) was found to be the dominant domain, with 1069 genes. Analysis of the main sub family, serine threonine protein kinases through gene ontology (GO), cis element and miRNA targets analysis revealed that most of the genes were involved in various functions aimed at enhancing abiotic stress tolerance. Further analysis of the RNA sequence data and qRT-PCR validation revealed 16 putative genes, which were highly up regulated under drought stress condition, and were found to be targeted by ghr-miR169a and ghr-miR164, previously associated with NAC(NAM, ATAF1/2 and CUC2) and myeloblastosis (MYB), the top rank drought stress tolerance genes. These genes can be exploited further to aid in development of more drought tolerant cotton genotypes.
Highlights
Cotton has been the number one source of natural fibre, which over the centuries been the indispensable raw material for textile industries globally [1]
The map generated showed that the logarithm of odds (LOD) values were above the noise level
An upland cotton, is the most preferred tetraploid cotton, due to its high yielding and comparatively good fibre qualities, but its production is threatened by its narrow genetic base, as a result of intensive selection and inbreeding
Summary
Cotton has been the number one source of natural fibre, which over the centuries been the indispensable raw material for textile industries globally [1]. For a long period of time, breeding and intensive selection for desirable agronomic traits has negatively affected the diversity, and reduced the genetic diversity of the modern cotton genotypes [3]. Cotton being a mesophytic plant, its production and fibre quality has been greatly affected by various abiotic and biotic stresses globally [4]. The development of more abiotic stress resilient cotton varieties has become a difficult due to the narrow genetic diversity of the available elite cultivars [5]. Cotton has been described as a relatively tolerant crop, the rate of salinization of the arable land and diminishing level of fresh water for agriculture compound the desire to have super performing cotton genotypes, with higher productivity in saline soil, and with higher water use efficiency [6]
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