Called genotypes (chromosome 1) from Illumina whole-genome sequencing of an Indica x Japonica rice F2 population

Motivation: Genotyping of bi-parental populations can be performed with low-coverage next-generation sequencing (LC-NGS). This allows the creation of highly saturated genetic maps at reasonable cost, precisely localized recombination breakpoints (i.e., the crossovers), and minimized mapping intervals for quantitative-trait locus analysis. LC-NGS data usually need to be imputed. Here we present imputed genotypes for rice chromosome 1 obtained from Illumina whole-genome low-coverage sequencing of an Indica x Japonica rice F2 bi-parental population (n = 222). The parents are IR64 (indica) and Azucena (tropical japonica). The genotypes were called with FreeBayes, using a SnakeMake pipeline.

动机：通过低覆盖度下一代测序（LC-NGS）对双亲种群进行基因分型，能够在合理的成本下创建高度饱和的遗传图谱，精确定位重组断裂点（即交叉点），并最小化定量性状位点分析的图谱区间。LC-NGS数据通常需要进行推断。在此，我们展示了从Indica x Japonica水稻F2双亲种群中获取的、通过Illumina全基因组低覆盖度测序得到的稻染色体1的推断基因型。亲本为IR64（Indica品种）和Azucena（热带Japonica品种）。基因型调用采用FreeBayes，并使用SnakeMake管道进行。