Alanine aminotransferase controls seed dormancy in barley

Sato, Kazuhiro; Yamane, Minoru; Yamaji, Nami; Kanamori, Hajime; Tagiri, Akemi; Schwerdt, Julian G.; Fincher, Geoffrey B.; Matsumoto, Takashi; Takeda, Kazuyoshi; Komatsuda, Takao

doi:10.1038/ncomms11625

Cited by 119 publications

(137 citation statements)

References 46 publications

Supporting

Mentioning

125

Contrasting

Order By: Relevance

“…3). These results are in agreement with the expression profiles and organ specificity of Qsd1 in barley, as well as the rice Qsd1 ortholog [9]. The results also support the homeology of barley and wheat Qsd1 sequences observed in the present study.…”

Section: Discussionsupporting

confidence: 93%

Sequence differences in the seed dormancy gene Qsd1 among various wheat genomes

et al. 2017

Self Cite

View full text Add to dashboard Cite

BackgroundPre-harvest sprouting frequently occurs in Triticum aestivum (wheat) and Hordeum vulgare (barley) at the end of the maturity period due to high rainfall, particularly in Asian monsoon areas. Seed dormancy is a major mechanism preventing pre-harvest sprouting in these crops.ResultsWe identified orthologous sequences of the major Hordeum vulgare (barley) seed dormancy gene Qsd1 in hexaploid wheat cv. Chinese Spring by performing genomic clone sequencing, followed by transcript sequencing. We detected 13 non-synonymous amino acid substitutions among the three sub-genomes of wheat and found that the Qsd1 sequence in the B sub-genome is most similar to that in barley. The Qsd1 sequence in A genome diploid wheat is highly similar to that in the hexaploid A sub-genome. Wheat orthologs of Qsd1 showed closer similarities to barley Qsd1 than did those of other accessions in the DNA database. Like barley Qsd1, all three wheat Qsd1s showed embryo-specific gene expression patterns, indicating that barley and wheat Qsd1 share an orthologous origin. The alignment of four hexaploid wheat cultivars indicated that the amino acid sequences of three spring cultivars, Chinese Spring, Haruyo Koi, and Fielder, are exactly the same in each sub-genome. Only Kitahonami has three amino acid substitutions at the B sub-genome.ConclusionsKitahonami has a longer seed dormancy period than does Chinese Spring. Sequence polymorphisms between Chiniese Spring and Kitahonami in the B sub-genome may underlie the phenotypic differences in seed dormancy between these hexaploid wheat cultivars.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3880-6) contains supplementary material, which is available to authorized users.

show abstract

Section: Discussionsupporting

confidence: 93%

Sequence differences in the seed dormancy gene Qsd1 among various wheat genomes

et al. 2017

Self Cite

View full text Add to dashboard Cite

show abstract

“…Earlier, it has been successfully demonstrated by Sato et al . () that the previously reported candidate genes can be validated the previously reported candidate gene, followed by its use in improving target trait. Therefore, we advanced the same population in this study for applying QTL‐seq approach to perform high‐resolution trait mapping and identify genomic region(s) associated with FSD.…”

Section: Discussionmentioning

confidence: 97%

“…The DArT and DArTseq are useful genotyping approaches but they do not provide exact position of SNPs in the reference genome which is very much required for performing fine mapping, candidate gene discovery and marker development. Earlier, it has been successfully demonstrated by Sato et al (2016) that the previously reported candidate genes can be validated the previously reported candidate gene, followed by its use in improving target trait. Therefore, we advanced the same population in this study for applying QTL-seq approach to perform high-resolution trait mapping and identify genomic region(s) associated with FSD.…”

Section: Discussionmentioning

confidence: 98%

Whole‐genome resequencing‐based QTL‐seq identified candidate genes and molecular markers for fresh seed dormancy in groundnut

Kumar

Janila

Vishwakarma

et al. 2019

Plant Biotechnology Journal

View full text Add to dashboard Cite

Summary The subspecies fastigiata of cultivated groundnut lost fresh seed dormancy (FSD) during domestication and human‐made selection. Groundnut varieties lacking FSD experience precocious seed germination during harvest imposing severe losses. Development of easy‐to‐use genetic markers enables early‐generation selection in different molecular breeding approaches. In this context, one recombinant inbred lines (RIL) population (ICGV 00350 × ICGV 97045) segregating for FSD was used for deploying QTL‐seq approach for identification of key genomic regions and candidate genes. Whole‐genome sequencing (WGS) data (87.93 Gbp) were generated and analysed for the dormant parent (ICGV 97045) and two DNA pools (dormant and nondormant). After analysis of resequenced data from the pooled samples with dormant parent (reference genome), we calculated delta‐SNP index and identified a total of 10,759 genomewide high‐confidence SNPs. Two candidate genomic regions spanning 2.4 Mb and 0.74 Mb on the B05 and A09 pseudomolecules, respectively, were identified controlling FSD. Two candidate genes—RING‐H2 finger protein and zeaxanthin epoxidase—were identified in these two regions, which significantly express during seed development and control abscisic acid (ABA) accumulation. QTL‐seq study presented here laid out development of a marker, GMFSD1, which was validated on a diverse panel and could be used in molecular breeding to improve dormancy in groundnut.

show abstract

“…A specific role for Ala ATs had been related to seed dormancy (Sato et al . ) and to specific stress responses, especially oxygen deprivation and nitrogen limitation (Shrawat et al . ; Rocha et al .…”

Section: Introductionmentioning

confidence: 99%

The role of alanine and aspartate aminotransferases in C₄ photosynthesis

Schlüter

Bräutigam

Droz³

et al. 2018

Plant Biol J

View full text Add to dashboard Cite

Alanine and aspartate are essential transfer metabolites for C species of the NAD-malic enzyme and phosphoenolpyruvate carboxykinase subtype. To some degree both amino acids are also part of the metabolite shuttle in NADP-malic enzyme plants. In comparison with C species, the majority of C species are therefore characterised by enhanced expression and activity of alanine and aspartate aminotransferases (AT) in the photosynthetically active tissue. Both enzymes exist in multiple copies and have been found in different subcellular compartments. We tested whether different C species show preferential recruitment of enzymes from specific lineages and subcellular compartments. Phylogenetic analysis of alanine and aspartate ATs from a variety of monocot and eudicot C species and their C relatives was combined with subcellular prediction tools and analysis of the subsequent transcript amounts in mature leaves. Recruitment of aspartate AT from a specific subcellular compartment was strongly connected to the biochemical subtype. Deviation from the main model was however observed in Gynandropsis gynandra. The configuration of alanine AT generally differed in monocot and eudicot species. C monocots recruited an alanine AT from a specific cytosolic branch, but eudicots use alanine AT copies from a mitochondrial branch. Generally, plants display high plasticity in the setup of the C pathway. Beside the common models for the different C subtypes, individual solutions were found for plant groups or lineages.

show abstract

Alanine aminotransferase controls seed dormancy in barley

Cited by 119 publications

References 46 publications

Sequence differences in the seed dormancy gene Qsd1 among various wheat genomes

Sequence differences in the seed dormancy gene Qsd1 among various wheat genomes

Whole‐genome resequencing‐based QTL‐seq identified candidate genes and molecular markers for fresh seed dormancy in groundnut

The role of alanine and aspartate aminotransferases in C₄ photosynthesis

Contact Info

Product

Resources

About

Alanine aminotransferase controls seed dormancy in barley

Cited by 119 publications

References 46 publications

Sequence differences in the seed dormancy gene Qsd1 among various wheat genomes

Sequence differences in the seed dormancy gene Qsd1 among various wheat genomes

Whole‐genome resequencing‐based QTL‐seq identified candidate genes and molecular markers for fresh seed dormancy in groundnut

The role of alanine and aspartate aminotransferases in C4 photosynthesis

Contact Info

Product

Resources

About

The role of alanine and aspartate aminotransferases in C₄ photosynthesis