Genome-Wide Association Mapping of Salinity Tolerance at the Seedling Stage in a Panel of Vietnamese Landraces Reveals New Valuable QTLs for Salinity Stress Tolerance Breeding in Rice.

Thao Duc Le,Hien Thi Thu Vu,Tu Xuan Dinh,Françoise Lazennec,Linh Hien Tran,Giang Thi Hoang,Huong Thi Vu,Pascal Gantet,Xuan Hoi Pham,Khanh Le Nguyen,Anne-Aliénor Véry,Floran Gathignol

doi:10.3390/plants10061088

Abstract

Rice tolerance to salinity stress involves diverse and complementary mechanisms, such as the regulation of genome expression, activation of specific ion-transport systems to manage excess sodium at the cell or plant level, and anatomical changes that avoid sodium penetration into the inner tissues of the plant. These complementary mechanisms can act synergistically to improve salinity tolerance in the plant, which is then interesting in breeding programs to pyramidize complementary QTLs (quantitative trait loci), to improve salinity stress tolerance of the plant at different developmental stages and in different environments. This approach presupposes the identification of salinity tolerance QTLs associated with different mechanisms involved in salinity tolerance, which requires the greatest possible genetic diversity to be explored. To contribute to this goal, we screened an original panel of 179 Vietnamese rice landraces genotyped with 21,623 SNP markers for salinity stress tolerance under 100 mM NaCl treatment, at the seedling stage, with the aim of identifying new QTLs involved in the salinity stress tolerance via a genome-wide association study (GWAS). Nine salinity tolerance-related traits, including the salt injury score, chlorophyll and water content, and K+ and Na+ contents were measured in leaves. GWAS analysis allowed the identification of 26 QTLs. Interestingly, ten of them were associated with several different traits, which indicates that these QTLs act pleiotropically to control the different levels of plant responses to salinity stress. Twenty-one identified QTLs colocalized with known QTLs. Several genes within these QTLs have functions related to salinity stress tolerance and are mainly involved in gene regulation, signal transduction or hormone signaling. Our study provides promising QTLs for breeding programs to enhance salinity tolerance and identifies candidate genes that should be further functionally studied to better understand salinity tolerance mechanisms in rice.

Highlights

More than one third of cultivated lands are polluted by excess of salt (NaCl) [1].Sodium is a toxic element for plants and this is true for rice, which is often cultivated in river delta areas where irrigation water is increasingly frequently contaminated by sea water [2]
The data from the last trial were chosen for performing genome-wide association study (GWAS), for which the screening protocol was improved and standardized for the Vietnamese rice landrace panel and for the parameter measurement as described in the Materials and Methods section
We found a total of 100 colocalizations, of which 17 were detected by GWAS [22,23,24,25,26], and 83 other colocalizations were mapped in biparental populations [13,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45]

Summary

Introduction

Sodium is a toxic element for plants and this is true for rice, which is often cultivated in river delta areas where irrigation water is increasingly frequently contaminated by sea water [2]. Rice is the most important food crop, feeding more than three billion people in the world [3]. In Vietnam, rice occupies 85% of the total agricultural area [4]. Vietnam is one of the first rice exporters in the world and plays an important role in food supply security, in Asian countries [6,7]. The Mekong River Delta and Red River Delta are the main areas of rice production in Vietnam; the Mekong River Delta represents 50%

Methods

Results

Discussion

Conclusion