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Open AccessArticle

Genome-Wide Association Study (GWAS) for Mesocotyl Elongation in Rice (Oryza sativa L.) under Multiple Culture Conditions

1
CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute in Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
2
Collaborative Innovation Center of Henan Grain Crops and Key Laboratory of Rice Biology in Henan Province, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
3
Strategic Innovation Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
*
Authors to whom correspondence should be addressed.
Both authors contributed equally to this work.
Genes 2020, 11(1), 49; https://doi.org/10.3390/genes11010049
Received: 10 December 2019 / Revised: 25 December 2019 / Accepted: 27 December 2019 / Published: 31 December 2019
(This article belongs to the Special Issue Recent Advances in Genetics and Breeding of Major Staple Food Crops)
Mesocotyl is a crucial organ for pushing buds out of soil, which plays a vital role in seedling emergence and establishment in dry direct-seeded rice. However, the genetic mechanisms of mesocotyl elongation remains unclear. In our study, 208 rice accessions were used to identify the SNPs significantly associated with mesocotyl length under various culture conditions, including sand, water and soil. The mesocotyl length ranges from 0 to 4.88 cm, 0 to 3.99 cm and 0 to 4.51 cm in sand, water and soil covering, respectively. A total of 2,338,336 SNPs were discovered by re-sequencing of 208 rice accessions. Genome-wide association study (GWAS) based on mixed linear model (MLM) was conducted and 16 unique loci were identified on chromosomes 1, 2 (2), 3, 4, 5 (2), 6 (2), 7, 8, 9 (2) and 12 (3), respectively, explaining phenotypic variations ranging from 6.3 to 15.9%. Among these loci, 12 were stable across two or more environments. Ten out of the sixteen loci coincided with known genes or quantitative trait locus (QTL), whereas the other six were potentially novel loci. Furthermore, five high-confidence candidate genes related to mesocotyl elongation were identified on chromosomes 1, 3, 5, 9 and 12. Moreover, qRT-PCR analysis showed that all the five genes showed significant expression difference between short-mesocotyl accessions and long-mesocotyl accessions. This study provides new insights into the genetic architecture of rice mesocotyl, the associated SNPs and germplasms with long mesocotyl could be useful in the breeding of mechanized dry direct-seeded rice. View Full-Text
Keywords: dry direct-seeded rice; early vigor; QTL; candidate gene; phenotyping dry direct-seeded rice; early vigor; QTL; candidate gene; phenotyping
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MDPI and ACS Style

Liu, H.; Zhan, J.; Li, J.; Lu, X.; Liu, J.; Wang, Y.; Zhao, Q.; Ye, G. Genome-Wide Association Study (GWAS) for Mesocotyl Elongation in Rice (Oryza sativa L.) under Multiple Culture Conditions. Genes 2020, 11, 49. https://doi.org/10.3390/genes11010049

AMA Style

Liu H, Zhan J, Li J, Lu X, Liu J, Wang Y, Zhao Q, Ye G. Genome-Wide Association Study (GWAS) for Mesocotyl Elongation in Rice (Oryza sativa L.) under Multiple Culture Conditions. Genes. 2020; 11(1):49. https://doi.org/10.3390/genes11010049

Chicago/Turabian Style

Liu, Hongyan; Zhan, Junhui; Li, Jiaolong; Lu, Xiang; Liu, Jindong; Wang, Yamei; Zhao, Quanzhi; Ye, Guoyou. 2020. "Genome-Wide Association Study (GWAS) for Mesocotyl Elongation in Rice (Oryza sativa L.) under Multiple Culture Conditions" Genes 11, no. 1: 49. https://doi.org/10.3390/genes11010049

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