Exploring transposable elements-based markers to identify allelic variations underlying agronomic traits in rice

The impact of transposable elements on tomato diversity

10.1101/2020.06.04.133835 ◽

2020 ◽

Cited By ~ 2

Author(s):

Marisol Domínguez ◽

Elise Dugas ◽

Médine Benchouaia ◽

Basile Leduque ◽

José Jimenez-Gomez ◽

...

Keyword(s):

Transposable Elements ◽

Agronomic Traits ◽

Association Studies ◽

Low Frequency ◽

Genome Wide Association Studies ◽

Environmental Response ◽

Whole Genome Resequencing ◽

Wild Accessions ◽

Genetic Pool ◽

The Impact

ABSTRACTTomatoes come in a multitude of shapes and flavors despite a narrow genetic pool. Here, we leveraged whole-genome resequencing data available for 602 cultivated and wild accessions to determine the contribution of transposable elements (TEs) to tomato diversity. We identified 6,906 TE insertions polymorphisms (TIPs), which result from the mobilization of 337 distinct TE families. Most TIPs are low frequency variants and disproportionately located within or adjacent to genes involved in environmental response. In addition, we show that genic TE insertions tend to have strong transcriptional effects and can notably lead to the generation of multiple transcript isoforms. We also uncovered through genome-wide association studies (GWAS) ~180 TIPs associated with extreme variations in major agronomic traits or secondary metabolites. Importantly, these TIPs tend to affect loci that are distinct from those tagged by SNPs. Collectively, our findings suggest a unique and important role for TE mobilization in tomato diversification, with important implications for future breeding.

Download Full-text

Allelic Variations of a Light Harvesting Chlorophyll A/B-Binding Protein Gene (Lhcb1) Associated with Agronomic Traits in Barley

PLoS ONE ◽

10.1371/journal.pone.0037573 ◽

2012 ◽

Vol 7 (5) ◽

pp. e37573 ◽

Cited By ~ 35

Author(s):

Yanshi Xia ◽

Zhengxiang Ning ◽

Guihua Bai ◽

Ronghua Li ◽

Guijun Yan ◽

...

Keyword(s):

Chlorophyll A ◽

Protein Gene ◽

Light Harvesting ◽

Agronomic Traits ◽

Binding Protein ◽

Binding Protein Gene ◽

Allelic Variations

Download Full-text

The impact of transposable elements on tomato diversity

Nature Communications ◽

10.1038/s41467-020-17874-2 ◽

2020 ◽

Vol 11 (1) ◽

Cited By ~ 5

Author(s):

Marisol Domínguez ◽

Elise Dugas ◽

Médine Benchouaia ◽

Basile Leduque ◽

José M Jiménez-Gómez ◽

...

Keyword(s):

Transposable Elements ◽

Agronomic Traits ◽

Association Studies ◽

Low Frequency ◽

Genome Wide Association Studies ◽

Environmental Responses ◽

Whole Genome Resequencing ◽

Wild Accessions ◽

Genetic Pool ◽

The Impact

Abstract Tomatoes come in a multitude of shapes and flavors despite a narrow genetic pool. Here, we leverage whole-genome resequencing data available for 602 cultivated and wild accessions to determine the contribution of transposable elements (TEs) to tomato diversity. We identify 6,906 TE insertions polymorphisms (TIPs), which result from the mobilization of 337 distinct TE families. Most TIPs are low frequency variants and TIPs are disproportionately located within or adjacent to genes involved in environmental responses. In addition, genic TE insertions tend to have strong transcriptional effects and they can notably lead to the generation of multiple transcript isoforms. Using genome-wide association studies (GWAS), we identify at least 40 TIPs robustly associated with extreme variation in major agronomic traits or secondary metabolites and in most cases, no SNP tags the TE insertion allele. Collectively, these findings highlight the unique role of TE mobilization in tomato diversification, with important implications for breeding.

Download Full-text

A Genetic Resource for Rice Improvement：introgression Library of Agronomic Traits for All AA Genome Species in Genus Oryza

10.21203/rs.3.rs-174988/v1 ◽

2021 ◽

Author(s):

Yu Zhang ◽

Jiawu Zhou ◽

Xu Peng ◽

Jing Li ◽

Xianneng Deng ◽

...

Keyword(s):

Agronomic Traits ◽

Genetic Dissection ◽

Genome Species ◽

Grain Length ◽

Aa Genome ◽

Grain Width ◽

Multiple Donors ◽

Rice Improvement ◽

Allelic Variations ◽

Introgression Library

Abstract Background: Rice improvement depends on the availability of genetic variation, and AA genome Oryza species are the natural reservoir of favorable genes which are useful for rice breeding. Developing the introgression library using multiple AA genome species was rarely reported.Results: In this study, to systematically evaluate and utilize potentially valuable QTLs/genes or allelic variations, based on the evaluation and selection of agronomic traits, 6372 introgression lines (ILs) were raised by crossing 330 accessions of 7 AA genome species as the donor parents, with three elite cultivars of O. sativa, Dianjingyou 1, Yundao 1 and RD23 as the recurrent parents, respectively. Further, twenty-six, twenty-six and nineteen loci were detected in the multiple donors using 1,401 ILs in the Dianjingyou 1 background for grain length, grain width, and the ratio of grain length to grain width, respectively. Interestingly, ten loci had opposite effect on grain length in the different donors, so did grain width. Moreover, one locus for grain width, qGW3.1, was validated using the segregation population derived from the donor of O. glumaepatula. Conclusions: This introgression library provided the powerful resource for future rice improvement and genetic dissection of allelic variations. Selections of favorable alleles that are present in wild relatives proceed the driving force of the rice domestication.

Download Full-text

The relationship between allelic variations ofVrn-1andPpd-1and agronomic traits in Korean wheat cultivars

Indian Journal of Genetics and Plant Breeding (The) ◽

10.5958/0975-6906.2015.00046.2 ◽

2015 ◽

Vol 75 (3) ◽

pp. 294 ◽

Cited By ~ 1

Author(s):

Eun Jin Cho ◽

Chon-Sik Kang ◽

Young Mi Yoon ◽

Park Chul Soo

Keyword(s):

Agronomic Traits ◽

Wheat Cultivars ◽

Allelic Variations ◽

The Relationship

Download Full-text

Development of an Aus-Derived Nested Association Mapping (Aus-NAM) Population in Rice

Plants ◽

10.3390/plants10061255 ◽

2021 ◽

Vol 10 (6) ◽

pp. 1255

Author(s):

Justine K. Kitony ◽

Hidehiko Sunohara ◽

Mikako Tasaki ◽

Jun-Ichi Mori ◽

Akihisa Shimazu ◽

...

Keyword(s):

Qtl Mapping ◽

Association Mapping ◽

Genome Wide Association Study ◽

Genetic Resource ◽

Agronomic Traits ◽

Single Family ◽

Nested Association Mapping ◽

Flowering Genes ◽

Common Parent ◽

Allelic Variations

A genetic resource for studying genetic architecture of agronomic traits and environmental adaptation is essential for crop improvements. Here, we report the development of a rice nested association mapping population (aus-NAM) using 7 aus varieties as diversity donors and T65 as the common parent. Aus-NAM showed broad phenotypic variations. To test whether aus-NAM was useful for quantitative trait loci (QTL) mapping, known flowering genes (Ehd1, Hd1, and Ghd7) in rice were characterized using single-family QTL mapping, joint QTL mapping, and the methods based on genome-wide association study (GWAS). Ehd1 was detected in all the seven families and all the methods. On the other hand, Hd1 and Ghd7 were detected in some families, and joint QTL mapping and GWAS-based methods resulted in weaker and uncertain peaks. Overall, the high allelic variations in aus-NAM provide a valuable genetic resource for the rice community.

Download Full-text