title: Genome-wide Association Study (GWAS) of mesocotyl elongation based on re-sequencing approach in rice.
abstract: BACKGROUND
  Mechanized dry seeded rice can save both labour and water resources. Rice seedling establishment is sensitive to sowing depth while mesocotyl elongation facilitates the emergence of deeply sown seeds.
  
  
  RESULTS
  A set of 270 rice accessions, including 170 from the mini-core collection of Chinese rice germplasm (C Collection) and 100 varieties used in a breeding program for drought resistance (D Collection), was screened for mesocotyl lengths of seedlings grown in water (MLw) in darkness and in 5 cm sand culture (MLs). Twenty six accessions (10.53 %) have MLw longer than 1.0 cm. Eleven accessions had the highest mesocotyl lengths, i.e. 1.4 - 5.05 cm of MLw and 3.0 - 6.4 cm in 10 cm sand culture, including 7 upland landraces or varieties. The genotypic data of 1,019,883 SNPs were developed by re-sequencing of those accessions. A whole-genome SNP array (Rice SNP50) was used to genotype 24 accessions as a validation panel, giving 98.41 % of consistent SNPs with the re-sequencing data in average. GWAS based on compressed mixed linear model was conducted using GAPIT. Based on a threshold of -log(P) ≥8.0, 13 loci were associated to MLw on rice chromosome 1, 3, 4, 5, 6 and 9, respectively. Three associated loci, on chromosome 3, 6, and 10, were detected for MLs. A set of 99 associated SNPs for MLw, based on a compromised threshold (-log(P) ≥7.0), located in intergenic regions or different positions of 36 annotated genes, including one cullin and one growth regulating factor gene.
  
  
  CONCLUSIONS
  Higher proportion and extension of elongated mesocotyls were observed in the mini-core collection of rice germplasm and upland rice landraces or varieties, possibly causing the correlation between mesocotyl elongation and drought resistance. GWAS found 13 loci for mesocotyl length measured in dark germination that confirmed the previously reported co-location of two QTLs across populations and experiments. Associated SNPs hit 36 annotated genes including function-matching candidates like cullin and GRF. The germplasm with elongated mesocotyl, especially upland landraces or varieties, and the associated SNPs could be useful in further studies and breeding of mechanized dry seeded rice.
authors.affiliation: Shanghai Agrobiological Gene Center; Shanghai Research Station of Crop Gene Resource & Germplasm Enhancement, Chinese Ministry of Agriculture, Shanghai, 201106, China. wjh@sagc.org.cn.
authors.forename: Jinhong
authors.initials: J
authors.lastname: Wu
authors.affiliation: Shanghai Agrobiological Gene Center; Shanghai Research Station of Crop Gene Resource & Germplasm Enhancement, Chinese Ministry of Agriculture, Shanghai, 201106, China. ffj@sagc.org.cn.
authors.forename: Fangjun
authors.initials: F
authors.lastname: Feng
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China. xmlian@mail.hzau.edu.cn.
authors.forename: Xingming
authors.initials: X
authors.lastname: Lian
authors.affiliation: Shanghai Agrobiological Gene Center; Shanghai Research Station of Crop Gene Resource & Germplasm Enhancement, Chinese Ministry of Agriculture, Shanghai, 201106, China. txy081022@126.com.
authors.forename: Xiaoying
authors.initials: X
authors.lastname: Teng
authors.affiliation: Shanghai Agrobiological Gene Center; Shanghai Research Station of Crop Gene Resource & Germplasm Enhancement, Chinese Ministry of Agriculture, Shanghai, 201106, China. whb@sagc.org.cn.
authors.forename: Haibin
authors.initials: H
authors.lastname: Wei
authors.affiliation: Life Science and Technology Center, China National Seed Group Co., Ltd, Wuhan, China. yuhuihui@sinochem.com.
authors.forename: Huihui
authors.initials: H
authors.lastname: Yu
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China. xwbcn@webmail.hzau.edu.cn.
authors.forename: Weibo
authors.initials: W
authors.lastname: Xie
authors.affiliation: Shanghai Agrobiological Gene Center; Shanghai Research Station of Crop Gene Resource & Germplasm Enhancement, Chinese Ministry of Agriculture, Shanghai, 201106, China. myan@sagc.org.cn.
authors.forename: Min
authors.initials: M
authors.lastname: Yan
authors.affiliation: Shanghai Agrobiological Gene Center; Shanghai Research Station of Crop Gene Resource & Germplasm Enhancement, Chinese Ministry of Agriculture, Shanghai, 201106, China. 1009903008@qq.com.
authors.forename: Peiqing
authors.initials: P
authors.lastname: Fan
authors.affiliation: Shanghai Agrobiological Gene Center; Shanghai Research Station of Crop Gene Resource & Germplasm Enhancement, Chinese Ministry of Agriculture, Shanghai, 201106, China. fox.ly@foxmail.com.
authors.forename: Yang
authors.initials: Y
authors.lastname: Li
authors.affiliation: Shanghai Agrobiological Gene Center; Shanghai Research Station of Crop Gene Resource & Germplasm Enhancement, Chinese Ministry of Agriculture, Shanghai, 201106, China. mxs09@sagc.org.cn.
authors.forename: Xiaosong
authors.initials: X
authors.lastname: Ma
authors.affiliation: Shanghai Agrobiological Gene Center; Shanghai Research Station of Crop Gene Resource & Germplasm Enhancement, Chinese Ministry of Agriculture, Shanghai, 201106, China. lhy@sagc.org.cn.
authors.forename: Hongyan
authors.initials: H
authors.lastname: Liu
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China. ysb@mail.hzau.edu.cn.
authors.forename: Sibin
authors.initials: S
authors.lastname: Yu
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China. gwwang@mail.hzau.edu.cn.
authors.forename: Gongwei
authors.initials: G
authors.lastname: Wang
authors.affiliation: Life Science and Technology Center, China National Seed Group Co., Ltd, Wuhan, China. zhoufasong@sinochem.com.
authors.forename: Fasong
authors.initials: F
authors.lastname: Zhou
authors.affiliation: Shanghai Agrobiological Gene Center; Shanghai Research Station of Crop Gene Resource & Germplasm Enhancement, Chinese Ministry of Agriculture, Shanghai, 201106, China. lijun@sagc.org.cn.|National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China. lijun@sagc.org.cn.
authors.forename: Lijun
authors.initials: L
authors.lastname: Luo
authors.affiliation: Shanghai Agrobiological Gene Center; Shanghai Research Station of Crop Gene Resource & Germplasm Enhancement, Chinese Ministry of Agriculture, Shanghai, 201106, China. hmei@sagc.org.cn.
authors.forename: Hanwei
authors.initials: H
authors.lastname: Mei
mesh_terms: D055106:Genome-Wide Association Study; D012275:Oryza / Q000235:genetics* / Q000254:growth & development; D018520:Plant Shoots / Q000235:genetics / Q000254:growth & development; D020641:Polymorphism, Single Nucleotide; D036226:Seedlings / Q000235:genetics / Q000254:growth & development; D017422:Sequence Analysis, DNA