Molecular Mapping to Discover Reliable Salinity-Resilient QTLs from the Novel Landrace Akundi in Two Bi-Parental Populations Using SNP-Based Genome-Wide Analysis in Rice.

Achieving high-yield potential is always the ultimate objective of any breeding program. However, various abiotic stresses such as salinity, drought, cold, flood, and heat hampered rice productivity tremendously. Salinity is one of the most important abiotic stresses that adversely affect rice grain yield. The present investigation was undertaken to dissect new genetic loci, which are responsible for salt tolerance at the early seedling stage in rice. A bi-parental mapping population (F2:3) was developed from the cross between BRRI dhan28/Akundi, where BRRI dhan28 (BR28) is a salt-sensitive irrigated (boro) rice mega variety and Akundi is a highly salinity-tolerant Bangladeshi origin indica rice landrace that is utilized as a donor parent. We report reliable and stable QTLs for salt tolerance from a common donor (Akundi) irrespective of two different genetic backgrounds (BRRI dhan49/Akundi and BRRI dhan28/Akundi). A robust 1k-Rice Custom Amplicon (1k-RiCA) SNP marker genotyping platform was used for genome-wide analysis of this bi-parental population. After eliminating markers with high segregation distortion, 886 polymorphic SNPs built a genetic linkage map covering 1526.5 cM of whole rice genome with an average SNP density of 1.72 cM for the 12 genetic linkage groups. A total of 12 QTLs for nine different salt tolerance-related traits were identified using QGene and inclusive composite interval mapping of additive and dominant QTL (ICIM-ADD) under salt stress on seven different chromosomes. All of these 12 new QTLs were found to be unique, as no other map from the previous study has reported these QTLs in the similar chromosomal location and found them different from extensively studied Saltol, SKC1, OsSalT, and salT locus. Twenty-eight significant digenic/epistatic interactions were identified between chromosomal regions linked to or unlinked to QTLs. Akundi acts like a new alternate donor source of salt tolerance except for other usually known donors such as Nona Bokra, Pokkali, Capsule, and Hasawi used in salt tolerance genetic analysis and breeding programs worldwide, including Bangladesh. Integration of the seven novel, reliable, stable, and background independent salinity-resilient QTLs (qSES1, qSL1, qRL1, qSUR1, qSL8, qK8, qK1) reported in this investigation will expedite the cultivar development that is highly tolerant to salt stress.

Three QTL from Oryza meridionalis Could Improve Panicle Architecture in Asian Cultivated Rice.

Rice panicle architecture is directly associated with grain yield and is also the key target in high-yield rice breeding program. In this study, three BC6F2 segregation populations derived from the crosses between two accessions of Oryza meridionalis and a O. sativa spp. japonica cultivar Dianjingyou 1, were employed to map QTL for panicle architecture. Three QTL, EP4.2, DEP7 and DEP8 were identified and validated using substitution mapping strategy on chromosome 4, 9 and 8, respectively. The three QTL showed pleiotropic phenotype on panicle length (PL), grain number per panicle (GNPP), number of primary branches (NPB), number of secondary branches (NSB), and grain width. DEP7 and DEP8 showed yield-enhancing potential by increasing GNPP, NPB and NSB, while EP4.2 exhibited wide grain, short stalk and panicle which can improve plant and panicle architecture, too. Moreover, epistatic interaction for PL was detected between EP4.2 and DEP7, and epistatic analysis between DEP7 and DEP8 for GNPP and NPB also revealed significant two QTL interactions. The result would help us understand the molecular basis of panicle architecture and lay the foundation for using these three QTL in rice breeding.

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.

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.

Harnessing on Genetic Variability and Diversity of Rice (Oryza sativa L.) Genotypes Based on Quantitative and Qualitative Traits for Desirable Crossing Materials.

Yield is a complex parameter of rice due to its polygonal nature, sometimes making it difficult to coat the selection process in the breeding program. In the current study, 34 elite rice genotypes were assessed to evaluate 3 locations for the selection of desirable rice cultivars suitable for multiple environments based on genetic diversity. In variance analysis, all genotypes have revealed significant variations (p ≤ 0.001) for all studied characters, signifying a broader sense of genetic variability for selection purposes. The higher phenotypic coefficient of variation (PCV) and genotypic coefficient of variation (GCV) were found for yield-associated characteristics such as the number of grains panicle-1 (GP), panicles hill-1 (PPH), and tillers hill-1 (TILL). All of the characters had higher heritability (greater than 60%) and higher genetic advance (greater than 20%), which pointed out non-additive gene action and suggested that selection would be effective. The most significant traits causing the genotype variants were identified via principal component analysis. In the findings of the cluster analysis, 34 elite lines were separated into 3 categories of clusters, with cluster II being chosen as the best one. The relationship matrix between each elite cultivar and traits was also determined utilizing a heatmap. Based on multi-trait genotype-ideotype distance index (MGIDI), genotypes Gen2, Gen4, Gen14, Gen22, and Gen30 in Satkhira; Gen2, Gen6, Gen7, Gen15, and Gen30 in Kushtia; and Gen10, Gen12, Gen26, Gen30, and Gen34 in Barishal were found to be the most promising genotypes. Upon validation, these genotypes can be suggested for commercial release or used as potential breeding material in crossing programs for the development of cultivars suitable for multiple environments under the future changing climate.