Abstract
Productivity of rice, world's most important cereal is threatened by high temperature stress, intensified by climate change. Development of heat stress-tolerant varieties is one of the best strategies to maintain its productivity. However, heat stress tolerance is a multigenic trait and the candidate genes are poorly known. Therefore, we aimed to identify quantitative trait loci (QTL) for vegetative stage tolerance to heat stress in rice and the corresponding candidate genes. We used genotyping-by-sequencing to generate single nucleotide polymorphic (SNP) markers and genotype 150 F8 recombinant inbred lines (RILs) obtained by crossing heat tolerant “N22” and heat susceptible “IR64” varieties. A linkage map was constructed using 4,074 high quality SNP markers that corresponded to 1,638 recombinationally unique events in this mapping population. Six QTL for root length and two for shoot length under control conditions with 2.1–12% effect were identified. One QTL rlht5.1 was identified for “root length under heat stress,” with 20.4% effect. Four QTL were identified for “root length under heat stress as percent of control” that explained the total phenotypic variation from 5.2 to 8.6%. Three QTL with 5.3–10.2% effect were identified for “shoot length under heat stress,” and seven QTL with 6.6–19% effect were identified for “shoot length under heat stress expressed as percentage of control.” Among the QTL identified six were overlapping between those identified using shoot traits and root traits: two were overlapping between QTL identified for “shoot length under heat stress” and “root length expressed as percentage of control” and two QTL for “shoot length as percentage of control” were overlapping a QTL each for “root length as percentage of control” and “shoot length under heat stress.” Genes coding 1,037 potential transcripts were identified based on their location in 10 QTL regions for vegetative stage heat stress tolerance. Among these, 213 transcript annotations were reported to be connected to stress tolerance in previous research in the literature. These putative candidate genes included transcription factors, chaperone proteins (e.g., alpha-crystallin family heat shock protein 20 and DNAJ homolog heat shock protein), proteases, protein kinases, phospholipases, and proteins related to disease resistance and defense and several novel proteins currently annotated as expressed and hypothetical proteins.
Highlights
World population growth necessitates our best efforts to increase crop production by 50% before 2030 (Tomlinson, 2013)
Shoot and root growth of “IR64” at 37◦C represented only 4 and 18% of the sizes attained at mesothermic control temperature
As significant phenotypic differences were observed between “N22” and “IR64,” we further evaluated the high temperature root and shoot growth responses of a recombinant inbred population derived from these two genotypes
Summary
World population growth necessitates our best efforts to increase crop production by 50% before 2030 (Tomlinson, 2013). The efficiency of pollen production and anther dehiscence in rice varieties grown under heat stress have been shown to be reduced, compromising the number of pollen produced and pollen shedding (Prasad et al, 2006) Most of these studies have utilized the available natural genetic variation to study the physiology and genetics of heat stress tolerance in rice at the reproductive stage (Prasad et al, 2006; Jagadish and Pal, 2009; Jagadish et al, 2010a,b, 2013; Tenorio et al, 2013; Bahuguna et al, 2015; Glaubitz et al, 2015; Shi et al, 2015). A metabolomic and transcriptomic study focused on the floral organs implicated genes related to sugar supply being differently expressed between “N22” and heat stress sensitive variety “Moroberekan” (Li et al, 2015) These studies focused on reproductive stage, raise further questions about the genetic control of heat stress tolerance during other developmental stages in rice. It might be possible that different genes act during different developmental stages to confer tolerance to heat stress
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