Abstract
Segregation distortion (SD) is a genetic mechanism commonly found in segregating or stable populations. The principle behind this puzzles many researchers. The F2 generation developed from wild Gossypium darwinii and G. hirsutum CCRI12 species was used to investigate the possible transcription factors within the segregation distortion regions (SDRs). The 384 out of 2763 markers were distorted in 29 SDRs on 18 chromosomes. Good collinearity was observed among genetic and physical maps of G. hirsutum and G. barbadense syntenic blocks. Total 568 genes were identified from SDRs of 18 chromosomes. Out of these genes, 128 belonged to three top-ranked salt-tolerant gene families. The DUF597 contained 8 uncharacterized genes linked to Pkinase (PF00069) gene family in the phylogenetic tree, while 15 uncharacterized genes clustered with the zinc finger gene family. Two hundred thirty four miRNAs targeted numerous genes, including ghr-miR156, ghr-miR399 and ghr-miR482, while others targeted top-ranked stress-responsive transcription factors. Moreover, these genes were involved in the regulation of numerous stress-responsive cis-regulatory elements. The RNA sequence data of fifteen upregulated genes were verified through the RT-qPCR. The expression profiles of two highly upregulated genes (Gh_D01G2015 and Gh_A01G1773) in salt-tolerant G. darwinii showed antagonistic expression in G. hirsutum. The results indicated that salt-tolerant genes have been possibly transferred from the wild G. darwinii species. A detailed functional analysis of these genes can be carried out which might be helpful in the future for gene cloning, transformation, gene editing and the development of salt-resistant cotton varieties.
Highlights
Segregation distortion (SD) is deviation of the observed allelic frequencies at a locus from expected Mendelian ratio, of a given genotypic class in a segregating population
According to Chen et al [17], a genetic map entailed of 2922 markers amplifying 2763 loci were distributed into 26 linkage groups corresponding to 26 chromosomes [17]
Salt stress-related genes in segregation distortion regions of chromosomes were identified from genetic map of F2 generation in G. hirsutum CCR112-4/G.darwinii
Summary
Segregation distortion (SD) is deviation of the observed allelic frequencies at a locus from expected Mendelian ratio, of a given genotypic class in a segregating population. In the construction of a genetic map, some chromosomal regions exhibit segregating alleles by deviating their anticipated Mendelian ratios towards a particular allele. These alleles tend to cluster at small genomic regions within a chromosome, known as segregation distortion regions (SDRs). Distorted markers bring errors leading to disturbance in the orders of genetic markers and influence the calculation of genetic distance [1] It affects the genetic mapping of morphological characteristics [2]. Lu et al [3] identified 18 SDRs on 10 chromosomes of maize and 3 gametophytic genes were potentially acting as genetic prompts of SDRs [3]. SDRs in double haploid rice recombinant inbred has been detected on 9th chromosome [4]
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