Genome‐wide association studies to identify rice salt‐tolerance markers

Abstract

Salinity is an ever increasing menace that affects agriculture worldwide. Crops such as rice are salt sensitive, but its degree of susceptibility varies widely between cultivars pointing to extensive genetic diversity that can be exploited to identify genes and proteins that are relevant in the response of rice to salt stress. We used a diversity panel of 306 rice accessions and collected phenotypic data after short (6 h), medium (7 d) and long (30 d) salinity treatment (50 mm NaCl). A genome-wide association study (GWAS) was subsequently performed, which identified around 1200 candidate genes from many functional categories, but this was treatment period dependent. Further analysis showed the presence of cation transporters and transcription factors with a known role in salinity tolerance and those that hitherto were not known to be involved in salt stress. Localization analysis of single nucleotide polymorphisms (SNPs) showed the presence of several hundred non-synonymous SNPs (nsSNPs) in coding regions and earmarked specific genomic regions with increased numbers of nsSNPs. It points to components of the ubiquitination pathway as important sources of genetic diversity that could underpin phenotypic variation in stress tolerance.

Climate resilient crops for improving global food security and safety

“…Although the use of brackish and saline water could help alleviate the world's water problems, this option is only possible with the development of salt‐tolerant crops (Figure ) or management practices that alleviate salt stress. A number of manuscripts in this volume (Herzog et al, ; Joshi et al, ; Lakra, Kaur, Anwar, Pareek, & Pareek, ; Oyiga et al, ; Patishtan, Hartley, Fonseca de Carvalho, & Maathuis, ) describe how plants tolerate high levels of salt. Soil phytoremediation and tolerance to heavy metals are also highlighted (Fasani, Manara, Martini, Furini, & DalCorso, ).…”

“…To develop crops tolerant to salinity, it is essential to understand the underlying physiological, molecular, and biochemical mechanisms and identify related genes and gene networks. Patishtan et al () report the results of a genome‐wide association studies of salt‐related traits in 306 rice cultivars. An important region on chromosome 8 was identified that contains a number of genes related to the ubiquitination pathway (Patishtan et al, ).…”

“…Patishtan et al () report the results of a genome‐wide association studies of salt‐related traits in 306 rice cultivars. An important region on chromosome 8 was identified that contains a number of genes related to the ubiquitination pathway (Patishtan et al, ). The process of protein degradation is therefore proposed as a major target for improving salt tolerance in rice.…”

Genome‐wide association analysis of salinity responsive traits in Medicago truncatula

“…Apart from the progress noted above for soybean and Arabidopsis , little is known about the genes shaping natural variation in salinity tolerance in other species. A few traits affected by salinity stress have been investigated via GWAS with high density markers, including traits related to seed germination, growth rate, transpiration rate, and tissue Na + /K + contents in rice (Al‐Tamimi et al, ; Patishtan, Hartley, Fonseca de Carvalho, & Maathuis, ; Shi et al, ), and root growth in Arabidopsis (Kobayashi et al, ). However, no overlapping genes or common mechanisms have been identified among these studies, and none of the identified genes have been validated with respect to salinity tolerance.…”

GWAS Uncovers Differential Genetic Bases for Drought and Salt Tolerances in Sesame at the Germination Stage

“…It offers advantages over traditional linkage analyses, such as more accurate positioning and mapping, simultaneous assessments of multiple alleles at a locus and no requirement for linkage group construction [ 27 , 28 ]. It has been successfully applied in several crops such as alfalfa, Arabidopsis thaliana , soybean, maize, rice, asparagus bean, Brassica napus , etc., to dissect complex traits including salt and drought tolerance [ 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 ]. GWAS was also successfully applied in sesame to unravel the genetic basis of its high oil production and quality, and some other key agronomic traits by fully sequencing a population composed of 705 worldwide accessions [ 40 ].…”