Abstract
The present study aimed to characterize the simple sequence repeat markers in cotton using the cotton expressed sequence tags. A total of 111 EST-SSR polymorphic molecular markers with trinucleotide motifs were used to evaluate the 79 accessions of Gossypium L., (G. darwinii, 59 and G. barbadense, 20) collected from the Galapagos Islands. The allele number ranged from one to seven, with an average value of 2.85 alleles per locus, while polymorphism information content values varied from 0.008 to 0.995, with an average of 0.520. The discrimination power ranks high for the majority of the SSRs, with an average value of 0.98. Among 111 pairs of EST-SSRs and gSSRs, a total of 49 markers, comprising nine DPLs, one each of MonCGR, MUCS0064, and NAU1028, and 37 SWUs (D-genome), were found to be the best matched hits, similar to the 155 genes identified by BLASTx in the reference genome of G. barbadense, G. arboreum L., and G. raimondii Ulbr. Related genes GOBAR_DD21902, GOBAR_DD15579, GOBAR_DD27526, and GOBAR_AA04676 revealed highly significant expression 10, 15, 18, 21, and 28 days post-anthesis of fiber development. The identified EST-SSR and gSSR markers can be effectively used for mapping functional genes of segregating cotton populations, QTL identification, and marker-assisted selection in cotton breeding programs.
Highlights
Cotton (Gossypium L.) belongs to an allotetraploidy complex of angiosperms taxonomically related to the Gossypieae tribe; it is a part of the family Malvaceae
42 markers have the best similarity hits with 116 genes by using G. raimondii as the reference genome, while 46 markers were found to be best matched with 135 genes when G. arboreum was used as the reference genome
The physiochemical analysis of genes mined in this study indicated that genes have both hydrophobic and hydrophilic properties as the Grand Average of Hydropathy (GRAVY) values were found to range from −1 to 0.765, with a molecular weight ranging from 10.11 to 288.95 and an isoelectric point (PI) value in the range of −26.5 to 54 (Table S1)
Summary
Cotton (Gossypium L.) belongs to an allotetraploidy complex of angiosperms taxonomically related to the Gossypieae tribe; it is a part of the family Malvaceae. It is a major contributor of raw fibers, accounting for 95% of the world’s cotton [1]. Modern cotton cultivars are allotetraploid, G. hirsutum L., and G. barbadense, with chromosome numbers (n = 2x = 26) [2]. Agronomy 2018, 8, 181 indigenous D-genome diploids of the New World through transoceanic dispersal [2]. In order to sustain the inherited enhancements of major cultivated species, it is necessary to collect, evaluate, characterize, and conserve, either on-farm or ex situ, their biodiversity
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