Dataset Information

SlGID1a Is a Putative Candidate Gene for qtph1.1, a Major-Effect Quantitative Trait Locus Controlling Tomato Plant Height.

ABSTRACT: Plant height is an important agronomic trait in crops. Several genes underlying tomato (Solanum lycopersicum) plant height mutants have been cloned. However, few quantitative trait genes for plant height have been identified in tomato. In this study, seven quantitative trait loci (QTLs) controlling plant height were identified in tomato. Of which, qtph1.1 (QTL for tomato plant height 1.1), qtph3.1 and qtph12.1 were major QTLs and explained 15, 16, and 12% of phenotypic variation (R2), respectively. The qtph1.1 was further mapped to an 18.9-kb interval on chromosome 1. Based on the annotated tomato genome (version SL2.50, annotation ITAG2.40), Solyc01g098390 encoding GA receptor SlGID1a was the putative candidate gene. The SlGID1a gene underlying the qtph1.1 locus contained a single nucleotide polymorphism (SNP) that resulted in an amino acid alteration in protein sequence. The near-isogenic line containing the qtph1.1 locus (NIL-qtph1.1) exhibited shorter internode length and cell length than the wild type (NIL-WT). The dwarf phenotype of NIL-qtph1.1 could not be rescued by exogenous GA3 treatment. Transcriptome analysis and real-time quantitative reverse transcription PCR (qPCR) showed that several genes related to biosynthesis and signaling of GA and auxin were differentially expressed in stems between NIL-qtph1.1 and NIL-WT. These findings might pave the road for understanding the molecular regulation mechanism of tomato plant height.

SUBMITTER: Liu X

PROVIDER: S-EPMC7427465 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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SlGID1a Is a Putative Candidate Gene for qtph1.1, a Major-Effect Quantitative Trait Locus Controlling Tomato Plant Height.

Liu Xiaolin X Yang Wencai W Wang Jing J Yang Mengxia M Wei Kai K Liu Xiaoyan X Qiu Zhengkun Z van Giang Tong T Wang Xiaoxuan X Guo Yanmei Y Li Junming J Liu Lei L Shu Jinshuai J Du Yongchen Y Huang Zejun Z

Frontiers in genetics 20200807

Plant height is an important agronomic trait in crops. Several genes underlying tomato (Solanum lycopersicum) plant height mutants have been cloned. However, few quantitative trait genes for plant height have been identified in tomato. In this study, seven quantitative trait loci (QTLs) controlling plant height were identified in tomato. Of which, qtph1.1 (QTL for tomato plant height 1.1), qtph3.1 and qtph12.1 were major QTLs and explained 15, 16, and 12% of ph ...[more]

PMID: 32849843

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Project description:BackgroundCrown rust, caused by Puccinia coronata f. sp. avenae, is the most important disease of oat worldwide. Adult plant resistance (APR), based upon partial resistance, has proven to be a durable rust management strategy in other cereal rust pathosystems. The crown rust APR in the oat line MN841801 has been effective for more than 30 years. The genetic basis of this APR was studied under field conditions in three recombinant inbred line (RIL) populations: 1) AC Assiniboia/MN841801, 2) AC Medallion/MN841801, and 3) Makuru/MN841801. The populations were evaluated for crown rust resistance with the crown rust isolate CR251 (race BRBB) in multiple environments. The 6 K oat and 90 K wheat Illumina Infinium single nucleotide polymorphism (SNP) arrays were used for genotyping the AC Assiniboia/MN841801 population. KASP assays were designed for selected SNPs and genotyped on the other two populations.ResultsThis study reports a high density genetic linkage map constructed with oat and wheat SNP markers in the AC Assiniboia/MN841801 RIL population. Most wheat SNPs were monomorphic in the oat population. However the polymorphic wheat SNPs could be scored accurately and integrated well into the linkage map. A major quantitative trait locus (QTL) on oat chromosome 14D, designated QPc.crc-14D, explained up to 76% of the APR phenotypic variance. This QTL is flanked by two SNP markers, GMI_GBS_90753 and GMI_ES14_c1439_83. QPc.crc-14D was validated in the populations AC Medallion/MN841801 and Makuru/MN841801.ConclusionsWe report the first APR QTL in oat with a large and consistent effect. QPc.crc-14D was statistically significant in all environments tested in each of the three oat populations. QPc.crc-14D is a suitable candidate for use in marker-assisted breeding and also an excellent target for map-based cloning. This is also the first study to use the 90 K wheat Infinium SNP array on oat for marker development and comparative mapping. The Infinium SNP array is a useful tool for saturating oat maps with markers. Synteny with wheat suggests that QPc.crc-14D is orthologous with the stripe rust APR gene Yr16 in wheat.

Dataset Information

SlGID1a Is a Putative Candidate Gene for qtph1.1, a Major-Effect Quantitative Trait Locus Controlling Tomato Plant Height.

Publications

<i>SlGID1a</i> Is a Putative Candidate Gene for <i>qtph1.1</i>, a Major-Effect Quantitative Trait Locus Controlling Tomato Plant Height.

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