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Article

Genome-Wide Mining and Characterization of SSR Markers for Gene Mapping and Gene Diversity in Gossypium barbadense L. and Gossypium darwinii G. Watt Accessions

by
Allah Ditta
1,2,†,
Zhongli Zhou
1,†,
Xiaoyan Cai
1,
Muhammad Shehzad
1,
Xingxing Wang
1,
Kiflom Weldu Okubazghi
1,3,
Yanchao Xu
1,
Yuqing Hou
1,
Muhammad Sajid Iqbal
1,
Muhammad Kashif Riaz Khan
2,
Kunbo Wang
1,* and
Fang Liu
1,*
1
State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
2
Plant Breeding and Genetics Division, Cotton Group, Nuclear Institute for Agriculture and Biology (NIAB), Jhang Road, Faisalabad 38000, Punjab, Pakistan
3
Hamelmalo Agricultural College, Keren P.O. Box 397, Eritrea
*
Authors to whom correspondence should be addressed.
†
These authors contributed equally.
Agronomy 2018, 8(9), 181; https://doi.org/10.3390/agronomy8090181
Submission received: 4 August 2018 / Revised: 1 September 2018 / Accepted: 10 September 2018 / Published: 12 September 2018
(This article belongs to the Special Issue Cotton Breeding, Genetics and Genomics)
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Abstract

The present study aimed to characterize the simple sequence repeat markers in cotton using the cotton expressed sequence tags. A total of 111 EST-SSR polymorphic molecular markers with trinucleotide motifs were used to evaluate the 79 accessions of Gossypium L., (G. darwinii, 59 and G. barbadense, 20) collected from the Galapagos Islands. The allele number ranged from one to seven, with an average value of 2.85 alleles per locus, while polymorphism information content values varied from 0.008 to 0.995, with an average of 0.520. The discrimination power ranks high for the majority of the SSRs, with an average value of 0.98. Among 111 pairs of EST-SSRs and gSSRs, a total of 49 markers, comprising nine DPLs, one each of MonCGR, MUCS0064, and NAU1028, and 37 SWUs (D-genome), were found to be the best matched hits, similar to the 155 genes identified by BLASTx in the reference genome of G. barbadense, G. arboreum L., and G. raimondii Ulbr. Related genes GOBAR_DD21902, GOBAR_DD15579, GOBAR_DD27526, and GOBAR_AA04676 revealed highly significant expression 10, 15, 18, 21, and 28 days post-anthesis of fiber development. The identified EST-SSR and gSSR markers can be effectively used for mapping functional genes of segregating cotton populations, QTL identification, and marker-assisted selection in cotton breeding programs.
Keywords: SSR markers; Gossypium accessions; genes; gene diversity; polymorphism information content and discrimination power SSR markers; Gossypium accessions; genes; gene diversity; polymorphism information content and discrimination power

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MDPI and ACS Style

Ditta, A.; Zhou, Z.; Cai, X.; Shehzad, M.; Wang, X.; Okubazghi, K.W.; Xu, Y.; Hou, Y.; Sajid Iqbal, M.; Khan, M.K.R.; et al. Genome-Wide Mining and Characterization of SSR Markers for Gene Mapping and Gene Diversity in Gossypium barbadense L. and Gossypium darwinii G. Watt Accessions. Agronomy 2018, 8, 181. https://doi.org/10.3390/agronomy8090181

AMA Style

Ditta A, Zhou Z, Cai X, Shehzad M, Wang X, Okubazghi KW, Xu Y, Hou Y, Sajid Iqbal M, Khan MKR, et al. Genome-Wide Mining and Characterization of SSR Markers for Gene Mapping and Gene Diversity in Gossypium barbadense L. and Gossypium darwinii G. Watt Accessions. Agronomy. 2018; 8(9):181. https://doi.org/10.3390/agronomy8090181

Chicago/Turabian Style

Ditta, Allah, Zhongli Zhou, Xiaoyan Cai, Muhammad Shehzad, Xingxing Wang, Kiflom Weldu Okubazghi, Yanchao Xu, Yuqing Hou, Muhammad Sajid Iqbal, Muhammad Kashif Riaz Khan, and et al. 2018. "Genome-Wide Mining and Characterization of SSR Markers for Gene Mapping and Gene Diversity in Gossypium barbadense L. and Gossypium darwinii G. Watt Accessions" Agronomy 8, no. 9: 181. https://doi.org/10.3390/agronomy8090181

APA Style

Ditta, A., Zhou, Z., Cai, X., Shehzad, M., Wang, X., Okubazghi, K. W., Xu, Y., Hou, Y., Sajid Iqbal, M., Khan, M. K. R., Wang, K., & Liu, F. (2018). Genome-Wide Mining and Characterization of SSR Markers for Gene Mapping and Gene Diversity in Gossypium barbadense L. and Gossypium darwinii G. Watt Accessions. Agronomy, 8(9), 181. https://doi.org/10.3390/agronomy8090181

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