SSR-Linkage map of interspecific populations derived from Gossypium trilobum and Gossypium thurberi and determination of genes harbored within the segregating distortion regions

Abstract

Wild cotton species have significant agronomic traits that can be introgressed into elite cultivated varieties. The use of a genetic map is important in exploring, identification and mining genes which carry significant traits. In this study, 188 F2mapping individuals were developed from Gossypium thurberi (female) and Gossypium trilobum (male), and were genotyped by using simple sequence repeat (SSR) markers. A total of 12,560 simple sequence repeat (SSR) markers, developed by Southwest University, thus coded SWU were screened out of which only 994 were found to be polymorphic, and 849 markers were linked in all the 13 chromosomes. The map had a length of 1,012.458 cM with an average marker distance of 1.193 cM. Segregation distortion regions (SDRs) were observed on Chr01, Chr02, Chr06, Chr07 Chr09, Chr10 and Chr11 with a large proportion of the SDR regions segregating towards the heterozygous allele. There was good syntenic block formation that revealed good collinearity between the genetic and physical map of G. raimondii, compared to the Dt_sub genome of the G. hirsutum and G. barbadense. A total of 2,496 genes were mined within the SSR related regions. The proteins encoding the mined genes within the SDR had varied physiochemical properties; their molecular weights ranged from 6.586 to 252.737 kDa, charge range of -39.5 to 52, grand hydropathy value (GRAVY) of -1.177 to 0.936 and isoelectric (pI) value of 4.087 to 12.206. The low GRAVY values detected showed that the proteins encoding these genes were hydrophilic in nature, a property common among the stress responsive genes. The RNA sequence analysis revealed more of the genes were highly upregulated in various stages of fiber development for instance; Gorai.002G241300 was highly up regulated at 5, 10, 20 and 25 day post anthesis (DPA). Validation through RT-qPCR further revealed that these genes mined within the SDR regions might be playing a significant role under fiber development stages, therefore we infer that Gorai.007G347600 (TFCA), Gorai.012G141600 (FOLB1), Gorai.006G024500 (NMD3), Gorai.002G229900 (LST8) and Gorai.002G235200 (NSA2) are significantly important in fiber development and in turn the quality, and further researches needed to be done to elucidate their exact roles in the fiber development process. The construction of the genetic map between the two wild species paves away for the mapping of quantitative trait loci (QTLs) since the average distance between the markers is small, and mining of genes on the SSR regions will provide an insight in identifying key genes that can be introgressed into the cultivated cotton cultivars.

Genotyping-by-sequencing and multilocation evaluation of two interspecific backcross populations identify QTLs for yield-related traits in pigeonpea

“…Many alleles have shown segregation distortion across the 11 CcLGs in both BP-1 and BP-2. The severe segregation distortion in backcross populations developed using wild species is also observed in barley (Mora et al 2016), cotton (Li et al 2018), rice (Xu et al 1997), potato (Manrique-Carpintero et al 2016, etc. Therefore, as proposed by Malosetti et al (2011) for such populations with segregation distortion, kinship matrix was used for QTL identification.…”

Cytological and molecular characterizations of a novel 2A nullisomic line derived from a widely-grown wheat cultivar Zhoumai 18 conferring male sterility

“…PCR products were separated on an 8% PAGE gel with a standard DNA molecular weight marker in the first lane of the gel. The products were run at 60 W for about 1.0 h. Then the gel was removed from the apparatus and stained using the silver staining method ( Li et al, 2018b ). Primers used for SSR analysis are list in Table S2 .…”

Genetic Map Construction and Functional Characterization of Genes within the Segregation Distortion Regions (SDRs) in the F2:3 Populations Derived from Wild Cotton Species of the D Genome

“…The analysis of the SD from the genetic maps constructed from the diploid cotton of the D genome was conducted. The rst map was then developed from two closely related parents, G. klotzschianum and G. davidsonii (Kirungu et al 2018) and the second map developed from G. thurberi and G. trilobum (Li et al 2018), in either of the maps, the F 2:3 population used, the genotypic data from the two maps were combined to generate the consensus map, and the consensus map was was limited to the two maps, being the only available maps generated from the population developed from the wild cotton species of the D genome. The focus was on chromosome D 5 02 and chromosome D 5 07 which showed severe distortions of markers from the two maps.…”