Efficient cloning of genes for wheat yield component traits from QTLs via sequencing of the RIL population

Zhang, Mingxia; Han, Xu; Wang, Hui; Sun, Junsheng; Guo, Baojin; Gao, Minggang; Xu, Huiyan; Zhang, Guizhi; Li, Hongna; Cao, Xiaofeng; Li, Nannan; Xu, Yiru; Wu, Qun; Wang, Chunyang; Zhang, Guohua; Yuan, Yapei; Man, Junxia; Pu, Yanyan; Lv, Guangde; Qu, Chunyan; Sun, Jinjie; Cheng, Xiyong; Dong, Xinjuan; Kong, Fanmei; Zhao, Yan; An, Yanrong; Yuan, Yuanyuan; Guo, Ying; Li, Sishen

doi:10.1101/2024.02.22.574000

Cited by 2 publications

(3 citation statements)

References 62 publications

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“…This provides a method for gene cloning. Based on this idea, we constructed a map of unigenes using an RIL population and cloned seven yield component trait genes, TaIFABPL, TaDdRp, TaRLK, TaTD, TaTFC3, TaKMT and TaSPL17 ( Zhang et al., 2024 ), a plant height gene TaDHL ( Guo et al., 2022 ), and a quality gene XIP ( Sun et al., 2022 ) from QTLs. This approach could be an effective method for isolating genes originally from wheat.…”

Section: Discussionmentioning

confidence: 99%

Cloning a novel reduced-height (Rht) gene TaOSCA1.4 from a QTL in wheat

Lv,

Jin,

Wang

et al. 2024

Front. Plant Sci.

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Reducing plant height (PH) is one of the core contents of the “Green Revolution”, which began in the 1960s in wheat. A number of 27 reduced-height (Rht) genes have been identified and a great number of quantitative trait loci (QTLs) for PH have been mapped on all 21 chromosomes. Nonetheless, only several genes regulated PH have been cloned. In this study, we found the interval of QTL QPh-1B included an EST-SSR marker swes1079. According to the sequence of swes1079, we cloned the TaOSCA1.4 gene. We developed a CAPS marker to analyze the variation across a natural population. The result showed that the PH was significantly different between the two haplotypes of TaOSCA1.4–1B under most of the 12 environments and the average values of irrigation and rainfed conditions. This result further demonstrated that TaOSCA1.4 was associated with PH. Then, we validated the TaOSCA1.4 via RNAi technology. The average PHs of the wild-type (WT), RNAi lines 1 (Ri-1) and 2 (Ri-2) were 94.6, 83.6 and 79.2 cm, respectively, with significant differences between the WT and Ri-1 and Ri-2. This result indicated that the TaOSCA1.4 gene controls PH. TaOSCA1.4 is a constitutively expressed gene and its protein localizes to the cell membrane. TaOSCA1.4 gene is a member of the OSCA gene family, which regulates intracellular Ca2+ concentration. We hypothesized that knock down mutants of TaOSCA1.4 gene reduced regulatory ability of Ca2+, thus reducing the PH. Furthermore, the cell lengths of the knock down mutants are not significantly different than that of WT. We speculate that TaOSCA1.4 gene is not directly associated with gibberellin (GA), which should be a novel mechanism for a wheat Rht gene.

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Section: Discussionmentioning

confidence: 99%

Cloning a novel reduced-height (Rht) gene TaOSCA1.4 from a QTL in wheat

Lv,

Jin,

Wang

et al. 2024

Front. Plant Sci.

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“…The polymorphic unigenes were used to construct the UG-Map based on their physical positions. The final UG-Map included 31,445 polymorphic sub-unigenes, which represented 27,983 unigenes and 118,120 SNPs/InDels [40]. The mRNA expression levels for a SNP/InDel of candidate genes were determined by the number of reads mapped on the reference genome for all lines of TN18 or LM6 genotypes in the TL-RILs.…”

Section: Data Analysis Qtl Detection and Candidate Gene Identificationmentioning

confidence: 99%

“…We previously constructed a genetic map of unigenes (UG-Map) via the RNA sequencing of 'TN18 × LM6' recombinant inbred lines (RILs) [40]. The objective of this study was to perform QTL analysis for EGA resistance using this RIL population, and then to identify candidate genes from stable QTLs.…”

Section: Introductionmentioning

confidence: 99%

Identification of Candidate Genes for English Grain Aphid Resistance from QTLs Using a RIL Population in Wheat

Zhang,

Chen,

et al. 2024

Agronomy

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The English grain aphid (EGA) (Sitobion avenae F.) is one of the most destructive species of aphids in wheat- (Triticum aestivum L.) planting areas worldwide. Large quantities of insecticides are usually used to control aphid damage. The identification of new EGA-resistant genes is necessary for sustainable wheat production. The objective of this study was to identify candidate genes for EGA resistance from stable quantitative trait loci (QTLs). We previously constructed a genetic map of unigenes (UG-Map) with 31,445 polymorphic sub-unigenes via the RNA sequencing of ‘TN18 × LM6’ recombinant inbred lines (TL-RILs). The relative aphid index (RAI) for the TL-RILs was investigated for two growing seasons, with three measured times (MTs) in each season. Using the UG-Map, 43 candidate genes were identified from 22 stable QTLs, with an average of 1.95 candidate genes per QTL. Among the 34 candidate genes annotated in the reference genome Chinese Spring (CS) RefSeq v1.1, the homologous genes of seven candidate genes, TraesCS1A02G-319900, TraesCS1B02G397300, TraesCS2D02G460800, TraesCS4A02G015600LC, TraesCS5B02G329200, TraesCS-6A02G000600 and TraesCS6A02G418600LC have been previously reported to play roles in aphid resistance. This suggests that these genes are strongly associated with EGA resistance in wheat. The candidate genes in this study should facilitate the cloning of EGA-resistant genes and genetic improvement in wheat breeding programs.

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Efficient cloning of genes for wheat yield component traits from QTLs via sequencing of the RIL population

Cited by 2 publications

References 62 publications

Cloning a novel reduced-height (Rht) gene TaOSCA1.4 from a QTL in wheat

Cloning a novel reduced-height (Rht) gene TaOSCA1.4 from a QTL in wheat

Identification of Candidate Genes for English Grain Aphid Resistance from QTLs Using a RIL Population in Wheat

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