Heat Stress Tolerance in Rice (Oryza sativa L.): Identification of Quantitative Trait Loci and Candidate Genes for Seedling Growth Under Heat Stress
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 can...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2018-11-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fpls.2018.01578/full |
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| author | Newton Lwiyiso Kilasi Newton Lwiyiso Kilasi Jugpreet Singh Carlos Eduardo Vallejos Changrong Ye S. V. Krishna Jagadish Paul Kusolwa Bala Rathinasabapathi |
| author_facet | Newton Lwiyiso Kilasi Newton Lwiyiso Kilasi Jugpreet Singh Carlos Eduardo Vallejos Changrong Ye S. V. Krishna Jagadish Paul Kusolwa Bala Rathinasabapathi |
| author_sort | Newton Lwiyiso Kilasi |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-22T19:56:46Z |
| format | Article |
| id | doaj.art-c38bd6ab89994198a45471dbb4fdd79f |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-22T19:56:46Z |
| publishDate | 2018-11-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-c38bd6ab89994198a45471dbb4fdd79f2022-12-21T18:14:24ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2018-11-01910.3389/fpls.2018.01578373853Heat Stress Tolerance in Rice (Oryza sativa L.): Identification of Quantitative Trait Loci and Candidate Genes for Seedling Growth Under Heat StressNewton Lwiyiso Kilasi0Newton Lwiyiso Kilasi1Jugpreet Singh2Carlos Eduardo Vallejos3Changrong Ye4S. V. Krishna Jagadish5Paul Kusolwa6Bala Rathinasabapathi7Horticultural Sciences Department, University of Florida, Gainesville, FL, United StatesDepartment of Crop Science and Production, Sokoine University of Agriculture, Morogoro, TanzaniaHorticultural Sciences Department, University of Florida, Gainesville, FL, United StatesHorticultural Sciences Department, University of Florida, Gainesville, FL, United StatesInstitute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, ChinaDepartment of Agronomy, Kansas State University, Manhattan, KS, United StatesDepartment of Crop Science and Production, Sokoine University of Agriculture, Morogoro, TanzaniaHorticultural Sciences Department, University of Florida, Gainesville, FL, United StatesProductivity 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.https://www.frontiersin.org/article/10.3389/fpls.2018.01578/fullausgenotyping-by-sequencingNagina 22quantitative trait lociroot growthshoot growth |
| spellingShingle | Newton Lwiyiso Kilasi Newton Lwiyiso Kilasi Jugpreet Singh Carlos Eduardo Vallejos Changrong Ye S. V. Krishna Jagadish Paul Kusolwa Bala Rathinasabapathi Heat Stress Tolerance in Rice (Oryza sativa L.): Identification of Quantitative Trait Loci and Candidate Genes for Seedling Growth Under Heat Stress Frontiers in Plant Science aus genotyping-by-sequencing Nagina 22 quantitative trait loci root growth shoot growth |
| title | Heat Stress Tolerance in Rice (Oryza sativa L.): Identification of Quantitative Trait Loci and Candidate Genes for Seedling Growth Under Heat Stress |
| title_full | Heat Stress Tolerance in Rice (Oryza sativa L.): Identification of Quantitative Trait Loci and Candidate Genes for Seedling Growth Under Heat Stress |
| title_fullStr | Heat Stress Tolerance in Rice (Oryza sativa L.): Identification of Quantitative Trait Loci and Candidate Genes for Seedling Growth Under Heat Stress |
| title_full_unstemmed | Heat Stress Tolerance in Rice (Oryza sativa L.): Identification of Quantitative Trait Loci and Candidate Genes for Seedling Growth Under Heat Stress |
| title_short | Heat Stress Tolerance in Rice (Oryza sativa L.): Identification of Quantitative Trait Loci and Candidate Genes for Seedling Growth Under Heat Stress |
| title_sort | heat stress tolerance in rice oryza sativa l identification of quantitative trait loci and candidate genes for seedling growth under heat stress |
| topic | aus genotyping-by-sequencing Nagina 22 quantitative trait loci root growth shoot growth |
| url | https://www.frontiersin.org/article/10.3389/fpls.2018.01578/full |
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