Genetic map construction and functional characterization of genes within the segregation distortion regions (SDRs) in the F2:3 generation derived from wild cotton species of the D genome

Joy Nyangasi Kirungu; Richard Odongo Magwanga; Margaret Linyerera Shiraku; Pu Lu; Teame Gereziher Mehari; Yang Xiu; Zhongli Zhou; Yuanchao Xu; Yuqing Hou; Pengcheng Li; Yun Zhou; Xiaoyan Cai; Kunbo Wang; Fang Liu

doi:10.7287/peerj.preprints.27845v1

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

Joy Nyangasi Kirungu ¹, Richard Odongo Magwanga², Margaret Linyerera Shiraku³, Pu Lu¹, Teame Gereziher Mehari¹, Yang Xiu¹, Zhongli Zhou¹, Yuanchao Xu¹, Yuqing Hou¹, Pengcheng Li¹, Yun Zhou⁴, Xiaoyan Cai¹, Kunbo Wang¹, Fang Liu¹

1 Cotton Biology, State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, Henan 455000, China., Anyang, Henan, China

2 Cotton biology, State Key Laboratory of Cotton Biology/ Institute of Cotton Research, Chinese Academy of 15 Agricultural Sciences, Anyang, Henan 455000, China, Anyang, Henan, China

3 Cotton Biology, State Key Laboratory of Cotton Biology/ Institute of Cotton Research, Chinese Academy of 15 Agricultural Sciences, Anyang, Henan 455000, China, Anyang, Henan, China

4 Laboratory of Plant Stress Biology, School of Life Science, Henan University/State Key Laboratory of Cotton Biology/Henan Key Laboratory of Plant Stress Biology, Kaifeng, Henan 475004, China, Keifang, China

DOI: 10.7287/peerj.preprints.27845v1

Published: 2019-07-10
Accepted: 2019-07-10

Subject Areas: Agricultural Science, Bioinformatics, Genetics, Genomics, Molecular Biology
Keywords: Genetic Map, Genes, Cis-regulatory elements, Segregation Distortion Region, miRNA

Copyright: © 2019 Kirungu et al.
Licence: This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.

Cite this article: Kirungu JN, Magwanga RO, Shiraku ML, Lu P, Mehari TG, Xiu Y, Zhou Z, Xu Y, Hou Y, Li P, Zhou Y, Cai X, Wang K, Liu F. 2019. 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. PeerJ Preprints 7:e27845v1 https://doi.org/10.7287/peerj.preprints.27845v1

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 F_2:3generations 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 F_2:3populations 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.