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

Latyr Diouf,Richard Magwanga,Xiongming Du,Kimbembe Romy,Joy Kirungu,Zhaoe Pan,Yin Jia,Harun Or Rashid,Shou-Pu He,Wen-Fang Gong

doi:10.3390/ijms18122622

Abstract

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.

Highlights

It is estimated that over 6% of agricultural land is affected by salinity [1]
In regard to CCRI35 and NH, an average of 10 individual reads for each of the parents were mapped to the sequence of the cotton genome and totaled 13,695,154 and 13,496,550, respectively
A total average of 85,372 and 117,128 SNPs were identified in CCRI35 and NH, respectively

Summary

Introduction

It is estimated that over 6% of agricultural land is affected by salinity [1]. To satisfy the increasing population demand, it is becoming obligatory to use saline soils, either by reclamation or by growing salt-tolerant plants [2]. To mitigate the challenge of salt stress, selective breeding programs are adopted in order to improve the performance of the genotypes developed [3]. Using conventional breeding techniques to enhance genetic improvement has limitations due to low efficiency, slow speed, and being expensive for some traits like salt tolerance [4]. Molecular breeding, such as marker-assisted breeding (MAS) and genomic selection (GS), have the potential to overcome the inefficiencies of conventional breeding [5]

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