An omics strategy increasingly improves the discovery of genetic loci and genes for seed-coat color formation in soybean Article Swipe
Jian Song
,
Ruixin Xu
,
Qingyuan Guo
,
Caiyu Wu
,
Yinghui Li
,
Xuewen Wang
,
Jun Wang
,
Lijuan Qiu
·
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.21203/rs.3.rs-2641232/v1
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.21203/rs.3.rs-2641232/v1
The phenotypic color of seeds is a complex agronomic trait and has economic and biological significance. The genetic control and molecular regulation mechanisms have been extensively studied. Here, we used a multi-omics strategy to explore the color formation in soybean seeds at a big-data scale. We identified 13 large quantitative trait loci (QTL) for color with bulk segregating analysis in recombinant inbreeding lines. GWAS analysis of colors and decomposed attributes in 763 germplasms revealed associated SNP sites perfectly falling in five major QTL, suggesting inherited genetic control on color during natural selection. Further transcriptomics analysis before and after color accumulation revealed 182 differentially expression genes (DEGs) in the five QTL, including known genes CHS, MYB, and F3’H involved in pigment accumulation. More DEGs with consistently up- or down-regulation were identified as shared regulatory genes for two or more color formations while some DEGs were only for a specific color formation. For example, five up-regulated DEGs in QTL qSC-3 were in flavonoid biosynthesis responsible for black and brown seed. The DEG (Glyma.08G085400) was identified in the purple seed only, which encodes gibberellin 2-beta-dioxygenase in the metabolism of colorful terpenoids. The candidate genes are involved in flavonoid biosynthesis, transcription factor regulation, gibberellin and terpenoid metabolism, photosynthesis, ascorbate and aldarate metabolism, and lipid metabolism. Seven differentially expressed transcription factors were also found to regulate color formation, including a known MYB. The finds expand QTL and gene candidates for color formation, which could guide to breed better cultivars with designed colors.
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Metadata
- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.21203/rs.3.rs-2641232/v1
- https://www.researchsquare.com/article/rs-2641232/latest.pdf
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- References
- 60
- Related Works
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- OpenAlex ID
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All OpenAlex metadata
Raw OpenAlex JSON
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https://openalex.org/W4365509822Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.21203/rs.3.rs-2641232/v1Digital Object Identifier
- Title
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An omics strategy increasingly improves the discovery of genetic loci and genes for seed-coat color formation in soybeanWork title
- Type
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preprintOpenAlex work type
- Language
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enPrimary language
- Publication year
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2023Year of publication
- Publication date
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2023-04-14Full publication date if available
- Authors
-
Jian Song, Ruixin Xu, Qingyuan Guo, Caiyu Wu, Yinghui Li, Xuewen Wang, Jun Wang, Lijuan QiuList of authors in order
- Landing page
-
https://doi.org/10.21203/rs.3.rs-2641232/v1Publisher landing page
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https://www.researchsquare.com/article/rs-2641232/latest.pdfDirect link to full text PDF
- Open access
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YesWhether a free full text is available
- OA status
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greenOpen access status per OpenAlex
- OA URL
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https://www.researchsquare.com/article/rs-2641232/latest.pdfDirect OA link when available
- Concepts
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Coat, Biology, Gene, Computational biology, Biotechnology, Genetics, PaleontologyTop concepts (fields/topics) attached by OpenAlex
- Cited by
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0Total citation count in OpenAlex
- References (count)
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60Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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| referenced_works | https://openalex.org/W2077531841, https://openalex.org/W4309074432, https://openalex.org/W4311908178, https://openalex.org/W2067141790, https://openalex.org/W2598716280, https://openalex.org/W2149992227, https://openalex.org/W2099548770, https://openalex.org/W2145963591, https://openalex.org/W2589736107, https://openalex.org/W3097912998, https://openalex.org/W2102800469, https://openalex.org/W3149552940, https://openalex.org/W2042638359, https://openalex.org/W2011852418, https://openalex.org/W4282832699, https://openalex.org/W3041388775, https://openalex.org/W2119951970, https://openalex.org/W2117840022, https://openalex.org/W2747068608, https://openalex.org/W3109503472, https://openalex.org/W2046479301, https://openalex.org/W2170551349, https://openalex.org/W4281568046, https://openalex.org/W4292707607, https://openalex.org/W2979411921, https://openalex.org/W2807780209, https://openalex.org/W2119180969, https://openalex.org/W2124058835, https://openalex.org/W2157752701, https://openalex.org/W2161633633, https://openalex.org/W2073774152, https://openalex.org/W3217545623, https://openalex.org/W2070539328, https://openalex.org/W2327140262, https://openalex.org/W2098727127, https://openalex.org/W1977136280, https://openalex.org/W2791686911, https://openalex.org/W2107628071, https://openalex.org/W2617193254, https://openalex.org/W2467487062, https://openalex.org/W2184809167, https://openalex.org/W4206091291, https://openalex.org/W1803174582, https://openalex.org/W2109130025, https://openalex.org/W2118999270, https://openalex.org/W4235779303, https://openalex.org/W3156798346, https://openalex.org/W2890283234, https://openalex.org/W1983002021, https://openalex.org/W2921489632, https://openalex.org/W2171737606, https://openalex.org/W2936660199, https://openalex.org/W2752211047, https://openalex.org/W4289131488, https://openalex.org/W2100548069, https://openalex.org/W1993947614, https://openalex.org/W1984967637, https://openalex.org/W3123036880, https://openalex.org/W4295846743, https://openalex.org/W4231096068 |
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