SNP discovery in proso millet (Panicum miliaceum L.) using low‐pass genome sequencing

Abstract

Domesticated $10,000 years ago in northern China, Proso millet (Panicum miliaceum L.) is a climate-resilient and human health-promoting cereal crop. The genome size of this self-pollinated allotetraploid is 923 Mb. Proso millet seeds are an important part of the human diet in many countries. In the USA, its use is restricted to the birdseed and pet food market. Proso millet is witnessing gradual demand in the global human health and wellness food market owing to its health-promoting properties such as low glycemic index and gluten-free. The breeding efforts for developing improved proso millet cultivars are hindered by the dearth of genomic resources available to researchers. The publication of the reference genome and availability of costeffective NGS methodologies could lead to the identification of high-quality genetic variants, which can be incorporated into breeding pipelines. Here, we report the identification of single-nucleotide polymorphisms (SNPs) by low-pass (1Â) genome sequencing of 85 diverse proso millet accessions from 23 different countries. The 2 Â 150 bp Illumina paired-end reads generated after sequencing were aligned to the proso millet reference genome. The resulting sequence alignment information was used to call SNPs. We obtained 972,863 bi-allelic SNPs after quality filtering of the raw SNPs. These SNPs were used to assess the population structure and phylogenetic relationships among the accessions. Most of the accessions were found to be highly inbred with heterozygosity ranging between .05 and .20. Principal component analysis (PCA) showed that PC1 (principal component) and PC2 explained 19% of the variability in the population. PCA also clustered all the genotypes into three groups.A neighbor-joining tree clustered the genotypes into four distinct groups exhibiting diverse representation within the population. The SNPs identified in our study could be used for molecular breeding and genetics research (e.g., genetic and association mapping, and population genetics) in proso millet after proper validation.

Molecular characterization and SNP identification using genotyping-by-sequencing in high-yielding mutants of proso millet

“…Another study generated 1,882 SNPs and developed genome-wide SNP markers by using the GBS approach among 190 accessions ( Johnson et al., 2019 ). In a similar study, 85 diverse proso lines from 25 different countries were analyzed to identify SNPs and to study the diversity clustering of the accessions ( Khound et al., 2022 ). However, the efforts in the crop are far behind the major crops like rice and wheat.…”

Microsatellite-Based Genetic Diversity Analysis and Population Structure of Proso Millet (Panicum miliaceum L.) in Kazakhstan

“…Assessments of genetic diversity inGenBankcollections has significance for plant breeding programs and genetic resource conservation [19][20][21][22][23]. The proso millet genome is relatively small and sized at 923 megabases [24,25]. Population structure studies of agricultural cropgene pools based on genotyping is important for the genetic improvement of economically valuable traits [26].…”