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Int. J. Mol. Sci. 2017, 18(12), 2622;

High-Density Linkage Map Construction and Mapping of Salt-Tolerant QTLs at Seedling Stage in Upland Cotton Using Genotyping by Sequencing (GBS)

State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
Senegalese River Valley Development Agency (SAED), Saint-Louis Bp74, Senegal
School of Physical and Biological Sciences (SPBS), Jaramogi Oginga Odinga University of Science and Technology (JOOUST), Main Campus, P.O. Box 210-40601 Bondo, Kenya
Chinese National Rice Research Institute (CNRRI), Chinese Academy of Agricultural Sciences, Hangzhou 311400, China
Author to whom correspondence should be addressed.
Received: 30 October 2017 / Revised: 24 November 2017 / Accepted: 29 November 2017 / Published: 5 December 2017
(This article belongs to the Section Molecular Plant Sciences)
PDF [5217 KB, uploaded 20 December 2017]


Over 6% of agricultural land is affected by salinity. It is becoming obligatory to use saline soils, so growing salt-tolerant plants is a priority. To gain an understanding of the genetic basis of upland cotton tolerance to salinity at seedling stage, an intra-specific cross was developed from CCRI35, tolerant to salinity, as female with Nan Dan (NH), sensitive to salinity, as the male. A genetic map of 5178 SNP markers was developed from 277 F2:3 populations. The map spanned 4768.098 cM, with an average distance of 0.92 cM. A total of 66 QTLs for 10 traits related to salinity were detected in three environments (0, 110, and 150 mM salt treatment). Only 14 QTLs were consistent, accounting for 2.72% to 9.87% of phenotypic variation. Parental contributions were found to be in the ratio of 3:1, 10 QTLs from the sensitive and four QTLs from the resistant parent. Five QTLs were located in At and nine QTLs in the Dt sub-genome. Moreover, eight clusters were identified, in which 12 putative key genes were found to be related to salinity. The GBS-SNPs-based genetic map developed is the first high-density genetic map that has the potential to provide deeper insights into upland cotton salinity tolerance. The 12 key genes found in this study could be used for QTL fine mapping and cloning for further studies. View Full-Text
Keywords: upland cotton; high-density; salinity tolerance; QTL mapping; GBS upland cotton; high-density; salinity tolerance; QTL mapping; GBS

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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).

Supplementary materials

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    Description: Figure S1: Frequency distribution of the 10 traits measured under 3 treatments during 2 years Figure S2: Total QTLs (66) found in this study, asterisk means consistent QTLs

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Diouf, L.; Pan, Z.; He, S.-P.; Gong, W.-F.; Jia, Y.H.; Magwanga, R.O.; Romy, K.R.E.; Or Rashid, H.; Kirungu, J.N.; Du, X. High-Density Linkage Map Construction and Mapping of Salt-Tolerant QTLs at Seedling Stage in Upland Cotton Using Genotyping by Sequencing (GBS). Int. J. Mol. Sci. 2017, 18, 2622.

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