Discovery of new genetic determinants of morphological plasticity in rice roots and shoots under phosphate starvation using GWAS

Mai, Nga T. P.; Chung, Duc; Nguyen, Hiep Van; Le, Khang Quoc; Duong, Linh Viet; Tran, Tuan Anh; To, Huong Thi Mai

doi:10.1016/j.jplph.2020.153340

Cited by 20 publications

(20 citation statements)

References 46 publications

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“…We have also extended upon seven published GWAS (Hoang et al 2019a ; Hoang et al 2019b ; Mai et al 2020 ; Phung et al 2016 ; Ta et al 2018 ; To et al 2019 ; To et al 2020 ), which focussed on specific traits but used a smaller number of markers and a third of the samples from the Vietnamese dataset. We took a similar approach of carrying out the analysis on both the full panel and the Indica and Japonica subpanels.…”

Section: Discussionmentioning

confidence: 99%

“…These subpopulations were classified by region, ecosystem and grain-type using passport information (province and ecosystem) and phenotyping. This dataset had subsequently been used for genome-wide phenotype-genotype association studies (GWAS) relating to root development (Phung et al 2016 ), panicle architecture (Ta et al 2018 ), drought tolerance (Hoang et al 2019b ), leaf development (Hoang et al 2019a ) and jasmonate regulation (To et al 2019 ) and phosphate efficiency (Mai et al 2020 ; To et al 2020 ).…”

Section: Introductionmentioning

confidence: 99%

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Resequencing of 672 Native Rice Accessions to Explore Genetic Diversity and Trait Associations in Vietnam

Higgins

Santos

Khanh

et al. 2021

Rice

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Background Vietnam possesses a vast diversity of rice landraces due to its geographical situation, latitudinal range, and a variety of ecosystems. This genetic diversity constitutes a highly valuable resource at a time when the highest rice production areas in the low-lying Mekong and Red River Deltas are enduring increasing threats from climate changes, particularly in rainfall and temperature patterns. Results We analysed 672 Vietnamese rice genomes, 616 newly sequenced, that encompass the range of rice varieties grown in the diverse ecosystems found throughout Vietnam. We described four Japonica and five Indica subpopulations within Vietnam likely adapted to the region of origin. We compared the population structure and genetic diversity of these Vietnamese rice genomes to the 3000 genomes of Asian cultivated rice. The named Indica-5 (I5) subpopulation was expanded in Vietnam and contained lowland Indica accessions, which had very low shared ancestry with accessions from any other subpopulation and were previously overlooked as admixtures. We scored phenotypic measurements for nineteen traits and identified 453 unique genotype-phenotype significant associations comprising twenty-one QTLs (quantitative trait loci). The strongest associations were observed for grain size traits, while weaker associations were observed for a range of characteristics, including panicle length, heading date and leaf width. Conclusions We showed how the rice diversity within Vietnam relates to the wider Asian rice diversity by using a number of approaches to provide a clear picture of the novel diversity present within Vietnam, mainly around the Indica-5 subpopulation. Our results highlight differences in genome composition and trait associations among traditional Vietnamese rice accessions, which are likely the product of adaption to multiple environmental conditions and regional preferences in a very diverse country. Our results highlighted traits and their associated genomic regions that are a potential source of novel loci and alleles to breed a new generation of low input sustainable and climate resilient rice.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Resequencing of 672 Native Rice Accessions to Explore Genetic Diversity and Trait Associations in Vietnam

Higgins

Santos

Khanh

et al. 2021

Rice

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“…We looked for the overlap of the selected regions with sets of QTLs previously reported in the literature (Supplementary Tables S4 and S5); 21 QTLs for basic plant and seed architecture traits identified using the same complete set of Vietnamese rice samples (Higgins el al.2021); and 88 QTLs associated with root development traits (Phung et al 2016), 29 QTLs for panicle morphological traits (Ta et al 2018), 17 QTLs for tolerance to water deficit (Hoang, Van Dinh, et al 2019), 13 QTLs for leaf mass traits (Hoang, Gantet, et al 2019), 25 QTLs for growth mediated by jasmonate (To et al 2019), 21 QTLs for phosphate starvation (Mai et al 2020) and 18 QTLs for phosphate efficiency (To et al 2020) reported for a subset of 180 samples of the whole dataset. The selected regions in the Japonica subpopulations had overlaps with all the QTLs sets, except QTLs associated with growth regulation by jasmonate (Supplementary Table S5).…”

Section: Methodsmentioning

confidence: 99%

“…QTLs from 8 published studies (Phung et al 2016; Ta et al 2018; To et al 2019; Hoang, Gantet, et al 2019; Hoang, Van Dinh, et al 2019; Mai et al 2020; To et al 2020) (Higgins et al) are plotted along each chromosome together with the 52 regions selected in the I5 subpopulation. The fourteen selected regions which overlap with at least one QTL are highlighted, the letters refer to the details shown in Table 2…”

Section: Methodsmentioning

confidence: 99%

“…To assess the putative role of these selected regions and whether these selected regions may contain loci that potentially could control agronomic traits, we looked for overlaps with previously mapped QTLs in the same diversity panel, and regions enriched in gene ontology (GO) terms. QTLs have been described for a range of agronomic traits using the complete set of 672 native rice accessions (Higgins et al 2021), while a subset of 182 of these traditional Vietnamese accessions (Phung 2014) were used for genome-wide phenotype-genotype association studies (GWAS) relating to root development (Phung et al 2016), panicle architecture (Ta et al 2018), drought tolerance (Hoang, Van Dinh, et al 2019), leaf development (Hoang, Gantet, et al 2019), Jasmonate regulation (To et al 2019) and phosphate starvation and efficiency (Mai et al 2020; To et al 2020). Finally, we studied alleles with non-synonymous substitutions in candidate genes in selected regions of the outlying and highly selected I5 subpopulation.…”

Section: Introductionmentioning

confidence: 99%

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Identifying genomic regions and candidate genes selected during the breeding of rice in Vietnam

Higgins

Santos

Khanh

et al. 2021

Preprint

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Background and aims: Vietnam harnesses a rich diversity of rice landraces adapted to a broad range of conditions, which constitute a largely untapped source of genetic diversity for the continuous improvement of rice cultivars. We previously identified a strong population structure in Vietnamese rice, which is captured in five Indica and four Japonica subpopulations, including an outlying Indica-5 group. Here, we leveraged on that strong differentiation, and the 672 rice genomes generated, to identify genes within genomic regions putatively selected during domestication and breeding of rice in Vietnam. Methodology: We identified significant distorted patterns in allele frequency (XP-CLR method) and population differentiation scores (FST), resulting from differential selective pressures between native subpopulations, and compared them with QTLs previously identified by GWAS in the same panel. We particularly focused on the outlying Indica-5 subpopulation because of its likely novelty and differential evolution. Results: We identified selection signatures in each of the Vietnamese subpopulations and carried out a comprehensive annotation of the 52 regions selected in Indica-5, which represented 8.1% of the rice genome. We annotated the 4,576 genes in these regions, verified the overlap with QTLs identified in the same diversity panel and the comparison with a FST analysis between subpopulations, to select sixty-five candidate genes as promising breeding targets, several of which harboured alleles with non-synonymous substitutions. Conclusions: Our results highlight genomic differences between traditional Vietnamese landraces, which are likely the product of adaption to multiple environmental conditions and regional culinary preferences in a very diverse country. We also verified the applicability of this genome scanning approach to identify potential regions harbouring novel loci and alleles to breed a new generation of sustainable and resilient rice.

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Pinpointing genomic regions associated with root system architecture in rice through an integrative meta-analysis approach

et al. 2021

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Discovery of new genetic determinants of morphological plasticity in rice roots and shoots under phosphate starvation using GWAS

Cited by 20 publications

References 46 publications

Resequencing of 672 Native Rice Accessions to Explore Genetic Diversity and Trait Associations in Vietnam

Resequencing of 672 Native Rice Accessions to Explore Genetic Diversity and Trait Associations in Vietnam

Identifying genomic regions and candidate genes selected during the breeding of rice in Vietnam

Pinpointing genomic regions associated with root system architecture in rice through an integrative meta-analysis approach

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