Genetic Mapping to Detect Stringent QTLs Using 1k-RiCA SNP Genotyping Platform from the New Landrace Associated with Salt Tolerance at the Seedling Stage in Rice

Abstract

Rice is the world’s most important food crop, providing the daily calorie intake for more than half of the world’s population. Rice breeding has always been preoccupied with maximizing yield potential. However, numerous abiotic factors, such as salt, cold, drought, and heat, significantly reduce rice productivity. Salinity, one of the major abiotic stresses, reduces rice yield worldwide. This study was conducted to determine new quantitative trait loci (QTLs) that regulate salt tolerance in rice seedlings. One F2:3 mapping population was derived from a cross between BRRI dhan49 (a popular but sensitive rainfed rice variety) and Akundi (a salt-tolerant rice landrace in Bangladesh used as a donor parent). The 1k-Rice Custom Amplicon (1k-RiCA) single-nucleotide polymorphism (SNP) markers were used to genotype this mapping population. After removing segregation distortion and monomorphic markers, 884 SNPs generated a 1526.8 cM-long genetic linkage map with a mean marker density of 1.7 cM for the 12 linkage groups. By exploiting QGene and ICIM-ADD, a sum of 15 QTLs for nine traits was identified in salt stress on seven chromosomes. Four important genomic loci were identified (qSES1, qSL1, qSUR1 and qRL1) on chromosome 1. Out of these 15 QTLs, 14 QTLs are unique, as no other study has mapped in the same chromosomal location. We also detected 15 putative candidate genes and their functions. The ICIM-EPI approach identified 43 significant pairwise epistasis interactions between regions associated with and unassociated with QTLs. Apart from more well-known donors, Akundi serves as an important new donor source for global salt tolerance breeding initiatives, including Bangladesh. The introgression of the novel QTLs identified in this study will accelerate the development of new salt-tolerant varieties that are highly resistant to salt stress using marker-enabled breeding.

Molecular Mapping To Identify Stable Salinity-Resilient QTLs From the Novel Landrace Akundi in Two Bi-Parental Populations Using SNP-Based 1k-RiCA Genotyping in Rice

“…In this study, the tolerant set had a high shoot length of 57.2 cm, which ranged from 55.8 cm to 58.6 cm, while the sensitive set had a shorter shoot length of 28.0 cm. The tolerant set also had more shoot biomass (0.21g), while the sensitive set had less (0.08g), which strongly supports that higher biomass and shoot length accelerate the growth at the seedling stage, which lowers the Na + concentration in the plant tissue [5,9,35].…”

“…Fifteen QTLs reported the mapping population derived from BR49/Akundi [5] and 12 QTLs controlling different salt-tolerant traits were identified from the present investigation using the population from BR28/Akundi cross. A total of seven QTLs (qSES1, qSL1, qRL1, qSUR1, qSL8, qK8, qK1) found stable that are colocated on chromosomes 1 and 8 detected from the same donor Akundi using two different F2:3 mapping populations derived from BR28/Akundi and BR49/Akundi (Table 3).…”

“…If the amount of Na + in the plant is high, water absorption is lower and plant growth is slowed down. This is because the plant cell's enzymatic connection is disrupted, which causes the plant to die early and reduces grain yield [5,9,34,35]. The tolerant plants had high percentage of survival (100%), but a lower percentage of survival (45%) found in the sensitive set.…”

“…The negative correlation was found among the SES score with K + concentration, root length and SPAD value; shoot and root length with Na+ concentration; and Na+/K+ ratio with K+ concentration, survival, shoot length and root length. In salt-stress conditions, a large amount of Na+ accumulated in the plant tissue causes severe cell damage consequently early plant death observed and also grain yield reduction occurred [5,35]. The correlation between the different variables (traits) helps us in the selection of progenies in the plant breeding program [36].…”

“…2 Salinity is key abiotic stress in this changed climatic condition that affects about one-third land areas of the world. Globally, salinity stress poses enormous challenges to food security [5]. Because the rice plant is basically sensitive to salt stress, increasing the level of salinity detrimentally affects productivity [6].…”