Genetic map construction and functional characterization of genes within the segregation distortion regions (SDRs) in the F_2:3 generation derived from wild cotton species of the D genome

Abstract

Segregation distortion (SD) is a phenomenon common among stable or segregating populations, and the principle behind it is still an issue that puzzles many researchers. An F2:3 generations developed from the wild cotton species of the D genomes was applied to investigate the possible plant transcription factors within the segregation distortion regions (SDRs). We constructed a consensus map between two maps in the D genome, map A; Gossypium klotzschianum and Gossypium davidsonii and Map B; Gossypium thurberi and Gossypium trilobum. The two maps were developed from 188 F2:3 populations for each map, a total of 1492 markers, were linked to the 13 linkage groups. The consensus linkage map size was 1467.445 cM with an average marker distance of 1.0370cM. Chr02 had the highest percentage of segregation distortion with 58.621% followed by Chr07 with 47.887%. A total of 6,038 genes were mined within the segregation distortion regions (SDR region) of Chr02 and Chr07 with 2,308 gene in Chr02 and 3,730 genes in Chr07, we obtained a total of 1,117 domains within the SDR with a total of 622 domains shared between the two chromosomes, the first 9 domains all belonged to the plant resistance genes (R genes), the largest domain was PF00069 with a total of 188 genes. A total of 287 miRNAs were found to target the various genes, such as gr-miR398, gra-miR5207, miR164a, miR164b, miR164c among others which have been found to target top-ranked stress-responsive transcription factors such as NAC genes. Moreover, the genes were found to be regulated by various stress responsive cis-regulatory elements. RNA profiling showed that higher numbers of genes were highly upregulated in abiotic and different fiber development stages. The result shows that the SDR regions could be playing an important role in the evolution of significant genes in plants.

Identification and characterization of genes related to salt stress tolerance within segregation distortion regions of genetic map in F2 population of upland cotton

“…that a higher number of SDRs were situated on chromosomes 02, 16 and 18 [60]. Similarly, Kirungu et al [16] observed the highest segregation distorted markers on chromosomes 02 and 07 in the genetic map of two wild cotton species., Chromosome 02 had the least mapped markers but had the highest percentage of segregation distortion, ranging between 42.8% and 76.08% [16]. Entire loci in SDR3-17 (Chr.17) and SDR20-23 (Chr23) diverged to G. darwinii, while 90% of the loci in four SDRs on D4 (Chr.22) and SDR21-23 (Chr23) deviated towards the female parent G. hirsutum CCRI12.…”

“…Previously, these methods have been employed by Ditta et al [31]. Meanwhile, the identified candidate genes from SSR markers found within SDRs had already been used by Kirungu et al [16]. The protein kinase, zinc finger and MYB domain of each gene were confirmed from SMART and PFAM databases (http://smart.emblheidelberg.de/; http://pfam.xfam.org).…”

“…Previously, several studies have been directed towards unraveling SDRs in cultivated cotton, but little research has been carried out on discovering these in F 2 population developed from wild cotton paternal species. Furthermore, insufficient research has concentrated on the determination of important genes harbored within SDRs [16]. Most recent effort in this regard has been done to develop a BC 2 F 2 population between Gossypium hirsutum and G. mustelinum exploring the SDRs in wild cotton progenitors [16].…”

“…Furthermore, insufficient research has concentrated on the determination of important genes harbored within SDRs [16]. Most recent effort in this regard has been done to develop a BC 2 F 2 population between Gossypium hirsutum and G. mustelinum exploring the SDRs in wild cotton progenitors [16]. In an earlier study, we developed a F 2 population of 188 individuals to generate a highly dense genetic map of 2763 polymorphic markers on all 26 chromosomes [17].…”

QTLs Identification for Iron Chlorosis in a Segregating Peach–Almond Progeny Through Double-Digest Sequence-Based Genotyping (SBG)

“…Although it has been described that the use of distorted markers could increase the genome coverage of the genetic maps (Zhang et al, 2007 , 2013 ; Cai et al, 2015 ) and it may be beneficial for QTL mapping (Xu, 2008 ; Zhang et al, 2010 ), many authors eliminate the skewed markers and they are not used for linkage maps construction, diminishing the information that it is possible to obtain. It has been proposed that the study of segregation distortion is significant because distorted markers may be linked to genes or traits of interest, and these genes may be beneficial or lethal to organisms (Kirungu et al, 2019 ). Then, the exclusion of such markers could bias the data and result in the loss of some important genetic information.…”