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

Pengcheng Li,Yingfan Cai,Fang Liu,Hejun Lu,Yuqing Hou,Xingxing Wang,Yuhong Wang,Pu Lu,Zhongli Zhou,Xiaoyan Cai,Richard Odongo Magwanga,Yun Zhou,Yanchao Xu,Renhai Peng,Joy Nyangasi Kirungu,Kunbo Wang,David D Fang

doi:10.1371/journal.pone.0207271

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.

Highlights

Cotton (Gossypium spp.) is the most important fiber crop and one of the sources for animal feeds and edible oil
Low levels of polymorphism have been reported in other plants for instance in peanut (6.8%) polymorphism was detected among the eSSRs, [35], maize (1.4%), rice (4.7%), sorghum (3.6%), wheat (3.2%) [36], in Gossypium species lower polymorphic rate of the eSSRs have been reported [37,38,39]
The eSSRs remain to be the markers of choice due to their ability to detect incomplete dominance inheritance, cost less and having a good genomic coverage despite the lower polymorphism observed in some plant [40]

Summary

Introduction

Cotton (Gossypium spp.) is the most important fiber crop and one of the sources for animal feeds and edible oil. Improving cotton yield and fiber quality is important for the survival of the cotton industry [2]. Serious outbreaks of diseases and pests have resulted in great loss in fibre production and its quality. Some of the useful alleles introgressed into elite cultivars have been achieved through interspecific hybridization for instance, improvement in fibre quality where, long fibre length upland cotton, G. hirsutum was achieved through tri-interspecific hybridization between G. thurberi, G. raimondii and G. barbadense [5]. Drought resistance in upland cotton has been achieved through the utilization of alleles from Asiatic Cottons [6]. Production of fertile hybrid germplasm with diploid Australian Gossypium species has been achieved [7]

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Discussion

Conclusion