Construction of a genetic map for pearl millet, Pennisetum glaucum (L.) R. Br., using a genotyping-by-sequencing (GBS) approach

Abstract

Pearl millet is the main component of traditional farming systems and a staple grain in the diet of sub-Saharan Africa and India. To facilitate breeding work in this crop, a genetic map consisting of single nucleotide polymorphism (SNP) markers was constructed using an F 2 population of 93 progenies, from a wild 9 cultivated pearl millet cross. We used a modified genotyping-by-sequencing (GBS) protocol involving two restriction enzymes (PstI-MspI) and PCR amplification with primers including three selective bases to generate 3,321 SNPs. Of these, 2,809 highquality SNPs exhibited a minor allele frequency C0.3. In total, 314 non-redundant haplotypes and 85 F 2 individuals were used to construct a genetic map spanning a total distance of 640 cM. These SNPs were evenly distributed over seven linkage groups ranging considerably in size (62-123 cM). The average density for this map was 0.51 SNP/cM, and the average interval between SNP markers was 2.1 (±0.6) cM. Finally, to establish bridges between the linkage groups of this and previous maps, 19 SSR markers were examined for polymorphism between the parents of this population. We could only tentatively suggest a correspondence between four of our linkage groups and those of previous maps. Overall, GBS enabled us to quickly produce a genetic map with a density and uniformity of markers greater than previously published maps. The availability of such a map will be useful for the identification of genomic regions associated with Striga resistance and other important agronomic traits.

Development of a High‐Density Linkage Map and Tagging Leaf Spot Resistance in Pearl Millet Using Genotyping‐by‐Sequencing Markers

“…Regions of significant segregation distortion have been reported in previous genetic mapping studies in pearl millet (Qi et al, 2004; Rajaram et al, 2013; Moumouni et al, 2015), so it is not surprising that they were detected in this population as well. However, we found two regions of segregation distortion in this population that each spans nearly an entire LG (LG 1 and LG 3) (Supplemental Fig.…”

“…The potential utility of GBS markers in developing high‐density molecular maps for several cereal crops, including maize, barley ( Hordeum vulgare L.) and oat ( Avena sativa L.) has been extensively reviewed and shown to be useful (He et al, 2014). Recently, a pearl millet linkage map was also developed with 2809 high‐quality SNP markers using a modified GBS protocol (Moumouni et al, 2015).…”

The Challenges and Opportunities Associated with Biofortification of Pearl Millet (Pennisetum glaucum) with Elevated Levels of Grain Iron and Zinc

“…This was achieved using a modified GBS platform, which involved two restriction enzymes ( PstI–MspI ) and PCR amplification with primers including three selective bases. These efforts resulted in 3,321 SNPs generated for public use (Moumouni et al, 2015). The availability of large numbers of SNP markers and high-density genetic maps will enhance the progress of gene and QTL mapping in biparental populations significantly, and facilitate association analyses on panels of unrelated lines.…”

Setaria viridis as a Model System to Advance Millet Genetics and Genomics

“…Although many quantitative trait loci (QTLs) have been identified for various agronomic traits such as plant height, flowering time, lodging, and drought tolerance (Mauro-Herrera et al, 2013; Parvathaneni et al, 2013; Sato et al, 2013; Babu et al, 2014; Qie et al, 2014; Mauro-Herrera and Doust, 2016; Rajput et al, 2016), the QTL intervals are often large (>1 Mb) and difficult to fine map. A partial solution is to generate high density linkage maps using technologies like genotyping by sequencing (Moumouni et al, 2015; Fang et al, 2016; Rajput et al, 2016), but the ultimate solution is to build high-quality reference genomes. To date, foxtail millet remains the only millet that has a chromosomal scale genome assembly (Bennetzen et al, 2012; Zhang et al, 2012), while Eragrostis tef has a draft genome (Cannarozzi et al, 2014), and the genome sequencing of finger millet and pearl millets are still ongoing ( Table 1 ).…”