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

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.

Genetic Structure and Geographical Differentiation of Traditional Rice (Oryza sativa L.) from Northern Vietnam

“…Northern Vietnam plays a significant role in these regions due to the vast genetic diversity resulting from its geographic situation and climate (varying from tropical conditions in the Red River Delta lowlands to subtropical climate conditions in the northeast highlands), the presence of many ethnic groups, and over 4000 years of rice cultivation experience [ 10 ]. Despite the abundant genetic resources, a few reports have been published relating to Vietnamese rice landraces with traits of interest, such as flowering time [ 11 ], drought tolerance [ 12 ], and salinity tolerance [ 13 ]. Recently, the resequencing of 672 native rice accessions was performed to explore genetic diversity and trait associations using the genome-wide association study (GWAS) approach [ 14 ].…”

An Overview of Abiotic Stress in Cereal Crops: Negative Impacts, Regulation, Biotechnology and Integrated Omics

“…In addition, the use of high-throughput techniques has been employed such as expression reads by RNA-Seq, random and targeted mutagenesis, gene shifting, complementation, and synthetic promoter trapping approaches make many avenues for functional analyses of AbS responsive genes and tolerance mechanisms [ 77 ]. Transcription factors (TFs) are crucially important in knowing the appropriate molecular processes and pathways that are involved in plant growth and survival under AbS conditions [ 78 , 79 , 80 ]. AbS are the quantitative and multiple genes associated in nature, these stress molecular cross-talks and their pathway interconnections are found under AbS conditions.…”

“…Similarly, some of the siRNAs play an important role as stress-inducers and affect protein synthesis including alternative splicing. The genome-wide association studies (GWAS) have become popular to provide novel strategies to identify and characterize the unique stress-responsive genes, which are introduced into crop plants and used in building up the tolerance against various AbS conditions [ 80 ]. In this record, the identification, and characterization of specific stress-responsive genes along with their promoters are analyzed for specificity.…”

Gene Mapping, Cloning and Association Analysis for Salt Tolerance in Rice

“…These studies showed that there were some genes expected to be involved in salt resistance in rice, including a nitrate transporter gene OsNRT2.1 [ 97 ], a MADS-box family transcription factor gene OsMADS31 [ 94 ], a sucrose transport protein gene OsSUT1 , a transcript factor gene OsGAMYB , and some function gene s OsCTR3 , OsMYB6 and OsHKT1;4 [ 88 ], etc. With the development of variety resequencing, salt tolerance GWAS has rapidly developed [ 98 , 99 , 100 , 101 , 102 , 103 , 104 , 105 ]. GWAS has exploited the natural variation in root architecture remodeling under salt tolerance to uncover the genetic controls underlying plant responses [ 83 , 106 ].…”