Reproductive tissues-specific meta-QTLs and candidate genes for development of heat-tolerant rice cultivars

Abstract

Rice holds the key to future food security. In rice-growing areas, temperature has already reached an optimum level for growth, hence, any further increase due to global climate change could significantly reduce rice yield. Several mapping studies have identified a plethora of reproductive tissue-specific and heat stress associated inconsistent quantitative trait loci (QTL), which could be exploited for improvement of heat tolerance. In this study, we performed a meta-analysis on previously reported QTLs and identified 35 most consistent meta-QTLs (MQTLs) across diverse genetic backgrounds and environments. Genetic and physical intervals of nearly 66% MQTLs were narrower than 5 cM and 2 Mb respectively, indicating hotspot genomic regions for heat tolerance. Comparative analyses of MQTLs underlying genes with microarray and RNA-seq based transcriptomic data sets revealed a core set of 45 heat-responsive genes, among which 24 were reproductive tissue-specific and have not been studied in detail before. Remarkably, all these genes corresponded to various stress associated functions, ranging from abiotic stress sensing to regulating plant stress responses, and included heat-shock genes (OsBiP2, OsMed37_1), transcription factors (OsNAS3, OsTEF1, OsWRKY10, OsWRKY21), transmembrane transporters (OsAAP7A, OsAMT2;1), sugar metabolizing (OsSUS4, α -Gal III) and abiotic stress (OsRCI2-7, SRWD1) genes. Functional data evidences from Arabidopsis heat-shock genes also suggest that OsBIP2 may be associated with thermotolerance of pollen tubes under heat stress conditions. Furthermore, promoters of identified genes were enriched with heat, dehydration, pollen and sugar responsive cis-acting regulatory elements, proposing a common regulatory mechanism might exist in rice for mitigating reproductive stage heat stress. These findings strongly support our results and provide new candidate genes for fast-track development of heat-tolerant rice cultivars. Key MessageBy integrating genetics and genomics data, reproductive tissues-specific and heat stress responsive 35 meta-QTLs and 45 candidate genes were identified, which could be exploited through marker-assisted breeding for fast-track development of heat-tolerant rice cultivars.

Consensus genomic regions associated with multiple abiotic stress tolerance in wheat and implications for wheat breeding

“…Out of 5,842 maize genes, 2,565 genes were available in 101 maize MQTL regions previously identified to be associated with drought stress tolerance 38,39,40 . Similarly, out of 5,277 rice genes, 2,704 genes belonged to 140 rice MQTLs earlier reported to be associated with heat, drought, and salinity stress tolerance 41,42,43,44,45 . The number of conserved genes at corresponding orthologous positions of MQTLs (between 'wheat and maize' and 'wheat and rice') ranged from just a few to hundreds of genes.…”

“…This analysis involved the following two steps: (i) gene models from the selected MQTL regions were BLASTed against rice and maize genomes at Ensemble Plants to discover conserved genomic regions, and (ii) the matching rice and maize orthologues were retrieved from the database with their genomic coordinates. In order to identify the ortho-MQTLs from the genomic regions conserved among all the three cereals, genomic positions of gene models underlying wheat MQTLs were compared with the orthologous genes available from rice MQTLs for SS tolerance 41 , DS tolerance 42,43 , HS tolerance 44,45 and maize MQTLs for DS tolerance 38,95,39,40 . MQTLs containing similar gene models located on conserved genomic regions of wheat, barley, rice, and maize were considered ortho-MQTLs.…”

When rice gets the chills: comparative transcriptome profiling at germination shows WRKY transcription factor responses

“…The OsWRKY21 gene, which was most highly differentially expressed between genotypes, could be a potential candidate in chilling tolerance. Despite recently discovered responsiveness to heat and drought stress (Raza et al 2020;Wang et al 2020) and to salicylic acid (Ramamoorthy et al 2008), there is little information on their role in chilling stress. Zhang et al (2012) also found that OsWRKY21 is highly expressed in response to chilling in rice seedlings.…”

Meta-QTLs, ortho-MQTLs and candidate genes for thermotolerance in wheat (Triticum aestivum L.)

“…A total of seven wheat MQTLs, each derived from ≥10 QTLs, were used for the identi cation of ortho-or syntenic MQTLs in rice. Following steps were involved: (i) genes detected in the above seven MQTLs were subjected to BLAST analysis against rice genome database at EnsemblPlants to identify rice orthologues, (ii) The rice orthologues were extracted with their physical positions from the database, (iii) Physical position of genes underlying wheat MQTLs were compared with the orthologous genes underlying rice MQTLs for heat tolerance (Raza et al 2020), and (iv) MQTLs harbouring similar genes located on known syntenic genomic positions of wheat and rice were considered as ortho-MQTLs.…”

“…Chromosomal regions carrying MQTLs that are conserved across more than one cereal were also identi ed. For this purpose, MQTLs for different traits relevant to thermotolerance in the present study in wheat were compared with MQTLs reported in rice (Raza et al 2020). Ortho-MQTLs could be identi ed for only seven wheat MQTLs positioned on chromosomes 1B, 2B, 2D, 3B, 7B, and 7D that correspond to rice-MQTLs (rMQTLs) located on rice chromosomes 1, 4, 5, 6, 7, and 8.…”