IC4R010-GWAS-2016-26612069

Project Title

Uncovering novel loci for mesocotyl elongation and shoot length in indica rice through genome-wide association mapping

To reduce spurious associations caused by population structure, a set of 469 global diverse indica accessions with rich genetic diversity (supplementary Table S1), representing the major rice-growing regions, was collected to construct a large association mapping population. All the samples were genotyped using a custom-designed array containing 5291 single nucleotide polymorphisms (SNPs)following the Infinium HD Assay Ultra Protocol (Illumina,Inc. San Diego, CA), with the minor allele frequency \5 % eliminated. Finally, 4136 SNPs were used in our GWAS analyses (supplementary Table S2). These accessions were planted in a randomized complete block design with three replications in a six-column 9 six-row area in Lingshui(LS; N18�320, E110�010) and Hangzhou (HZ; N30�150,E120�120) in 2014.

In this study, 469 indica accessions collected from 20 countries (Fig. 1a) were used as the GWAS panel The germplasm resources maintain rich mesocotyl elongation and shoot length variations (Fig. 1b–d), and the phenotypic variations are summarized in Table 1and supplementary Table S4.

In total, 52 accessions, which were divided into two groups, one with long and the other with short mesocotyl lengths, were selected to analyze the POE and SOE. SOE was the average POE per day before the germination rate stopped significantly increasing. The sowing depths of 2 and 5 cm represent shallow overburden and deep seeding,respectively. The results are summarized in Fig. 2.The mesocotyl lengths between the two groups were highly different independent of the sowing depth (Fig. 2a). For the 2-cm sowing depth, the POE of the long mesocotyl accessions was significantly greater than that of the short mesocotyl accessions, reaching 90.76 % (Fig. 2b).For the SOE trait, regardless of the sowing depth, the long mesocotyl group had a higher emergence rate than that of the short one (Fig. 2c).

Additionally, the correlations among POE, SOE, mesocotyl length and shoot length were analyzed, and the results showed that POE and SOE were highly positively correlated with mesocotyl length at 2- and 5-cm sowing depths (Fig. 3a, b).Moreover, in the deep soil condition,the POE and SOE were also positively correlated with shoot length, but the correlation coefficients were lower

than those of the mesocotyl length (Fig. 3b).

State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China