Identification of genomic regions governing moisture and heat stress tolerance employing association mapping in rice (Oryza sativa L.).

BACKGROUND: Rice crop is damaged extremely by abiotic stress world-wide. The best approach to enhance drought tolerance in rice varieties is to identify and introgress yield QTLs with major effects. The Association mapping approach helps in the identification of genomic regions governing physiological, yield and yield attributes under moisture and heat stress conditions in diverse collections of crop germplasm, based on historic recombination events and linkage disequilibrium across the genome. METHODS AND RESULTS: The association mapping panel of 110 rice germplasm lines exhibited significant variation for all the traits in both irrigated and moisture stress conditions. The extent of yield reduction ranged to 83% during rabi, 2018-19, 53% in rabi, 2019-20 and 68% in pooled analysis. The genotypes Badami, Badshabhog, Pankaj, Varalu, Vasundhara, Vivekdhan, Krishna and Minghui63 exhibited drought tolerance with least yield penalty under moisture stress conditions. The genotypes Konark, MTU3626, NLR33671, PR118 and Triguna exhibited minimal reduction in heat stress tolerance traits. Association mapping of germplasm using 37808 SNP markers detected a total of 10 major MTA (Marker-trait association) clusters distributed on chromosomes 1, 3, 4 and 11 through mixed linear model (MLM) governing multiple traits from individual data analysis which are consistent across the years and situations. The pooled data generated a total of five MTA clusters located on chromosome 6. In addition, several novel unique MTAs were also identified. Heat stress analysis generated a total of 23 MTAs distributed on chromosomes 1, 5, 6 and 11. Candidate gene analysis detected a total of 53 and 38 genes under individual and pooled data analysis for various yield and yield attributes under control and moisture stress conditions, respectively and a total of 11 candidate genes in heat stress Conditions. CONCLUSION: The major and novel MTAs identified in the present investigation for various drought and heat tolerant traits can be utilized for breeding climate-resilient rice varieties. The candidate genes predicted for key MTAs are of great value to deploy into the rice breeding after functional characterization.

Discovery of genomic regions and candidate genes for grain weight employing next generation sequencing based QTL-seq approach in rice (Oryza sativa L.).

Rice (Oryza sativa L.) yield enhancement is one of the prime objectives of plant breeders. Elucidation of the inheritance of grain weight, a key yield component trait, is of paramount importance for raising the yield thresholds in rice. In the present investigation, we employed Next-Generation Sequencing based QTL-seq approach to identify major genomic regions associated with grain weight using mapping populations derived from a cross between BPT5204 and MTU3626. QTL-seq analysis identified three grain weight quantitative trait loci (QTL) viz., qGW1 (35-40 Mb), qGW7 (10-18 Mb), and qGW8 (2-5 Mb) on chromosomes 1, 7 and 8, respectively and all are found to be novel. Further, qGW8 was confirmed through conventional QTL mapping in F2, F3 and BC1F2 populations and found to explain the phenotypic variance of 17.88%, 16.70% and 15.00%, respectively, indicating a major QTL for grain weight. Based on previous reports, two candidate genes in the qGW8 QTL were predicted i.e., LOC_Os08g01490 (Cytochrome P450), and LOC_Os08g01680 (WD domain, G-beta repeat domain containing protein) and through in silico analysis they were found to be highly expressed in reproductive organs during different stages of grain development. Here, we have demonstrated that QTL-seq is one of the rapid approaches to uncover novel QTLs controlling complex traits. The candidate genes identified in the present study undoubtedly enhance our understanding of the mechanism and inheritance of the grain weight. These candidate genes can be exploited for yield enhancement after confirmation through complementary studies.

Uncovering of natural allelic variants of key yield contributing genes by targeted resequencing in rice (Oryza sativa L.).

In rice (Oryza sativa L.), during the course of domestication, numerous beneficial alleles remain untapped in the progenitor wild species and landraces. This study aims at uncovering these promising alleles of six key genes influencing the yield, such as DEP1, Ghd7, Gn1a, GS3, qSW5 and sd1 by targeted resequencing of the 200 rice genotypes. In all, 543 nucleotide variations including single nucleotide polymorphisms and insertion and deletion polymorphisms were identified from the targeted genes. Of them, 225 were novel alleles, which identified in the present study only and 91 were beneficial alleles that showed significant association with the yield traits. Besides, we uncovered 128 population-specific alleles with indica being the highest of 79 alleles. The neutrality tests revealed that pleiotropic gene, Ghd7 and major grain size contributing gene, GS3 showed positive and balanced selection, respectively during the domestication. Further, the haplotype analysis revealed that some of the rice genotypes found to have rare haplotypes, especially the high yielding variety, BPT1768 has showed maximum of three genes such as Gn1a-8, qSW5-12 and GS3-29. The rice varieties with novel and beneficial alleles along with the rare haplotypes identified in the present study could be of immense value for yield improvement in the rice breeding programs.

Strigolactones are positive regulators of light-harvesting genes in tomato.

Strigolactones are newly identified plant hormones, shown to participate in the regulation of lateral shoot branching and root development. However, little is known about their effects on biological processes, genes, and proteins. Transcription profiling of roots treated with GR24, a synthetic strigolactone with proven biological activity, and/or indole acetic acid (IAA) was combined with physiological and transcriptional analysis of a tomato mutant (Sl-ORT1) deficient in strigolactone production. GR24 treatment led to markedly induced expression of genes putatively involved in light harvesting. This was apparent in both the presence and absence of exogenously applied IAA, but not with IAA treatment alone. Following validation of the microarray results, transcriptional induction by light of the GR24-induced genes was demonstrated in leaves exposed to high or low light intensities. Sl-ORT1 contained less chlorophyll and showed reduced expression of light harvesting-associated genes than the wild type (WT). Moreover, perfusion of GR24 into WT and Sl-ORT1 leaves led to induction of most of the examined light harvesting-associated genes. Results suggest that GR24 treatment interferes with the root's response to IAA treatment and that strigolactones are potentially positive regulators of light harvesting in plants.

A tomato strigolactone-impaired mutant displays aberrant shoot morphology and plant interactions.

Strigolactones are considered a new group of plant hormones. Their role as modulators of plant growth and signalling molecules for plant interactions first became evident in Arabidopsis, pea, and rice mutants that were flawed in strigolactone production, release, or perception. The first evidence in tomato (Solanum lycopersicon) of strigolactone deficiency is presented here. Sl-ORT1, previously identified as resistant to the parasitic plant Orobanche, had lower levels of arbuscular mycorrhizal fungus (Glomus intraradices) colonization, possibly as a result of its reduced ability to induce mycorrhizal hyphal branching. Biochemical analysis of mutant root extracts suggested that it produces only minute amounts of two of the tomato strigolactones: solanacol and didehydro-orobanchol. Accordingly, the transcription level of a key enzyme (CCD7) putatively involved in strigolactone synthesis in tomato was reduced in Sl-ORT1 compared with the wild type (WT). Sl-ORT1 shoots exhibited increased lateral shoot branching, whereas exogenous application of the synthetic strigolactone GR24 to the mutant restored the WT phenotype by reducing the number of lateral branches. Reduced lateral shoot branching was also evident in grafted plants which included a WT interstock, which was grafted between the mutant rootstock and the scion. In roots of these grafted plants, the CCD7 transcription level was not significantly induced, nor was mycorrhizal sensitivity restored. Hence, WT-interstock grafting, which restores mutant shoot morphology to WT, does not restore mutant root properties to WT. Characterization of the first tomato strigolactone-deficient mutant supports the putative general role of strigolactones as messengers of suppression of lateral shoot branching in a diversity of plant species.