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

Abstract

Pearl millet [Pennisetum glaucum (L.) R. Br; also Cenchrus americanus (L.) Morrone] is an important crop throughout the world but better genomic resources for this species are needed to facilitate crop improvement. Genome mapping studies are a prerequisite for tagging agronomically important traits. Genotyping-bysequencing (GBS) markers can be used to build high-density linkage maps, even in species lacking a reference genome. A recombinant inbred line (RIL) mapping population was developed from a cross between the lines 'Tift 99D 2 B 1 ' and 'Tift 454'. DNA from 186 RILs, the parents, and the F 1 was used for 96-plex ApeKI GBS library development, which was further used for sequencing. The sequencing results showed that the average number of good reads per individual was 2.2 million, the pass filter rate was 88%, and the CV was 43%. High-quality GBS markers were developed with stringent filtering on sequence data from 179 RILs. The reference genetic map developed using 150 RILs contained 16,650 single-nucleotide polymorphisms (SNPs) and 333,567 sequence tags spread across all seven chromosomes. The overall average density of SNP markers was 23.23 SNP/cM in the final map and 1.66 unique linkage bins per cM covering a total genetic distance of 716.7 cM. The linkage map was further validated for its utility by using it in mapping quantitative trait loci (QTLs) for flowering time and resistance to Pyricularia leaf spot [Pyricularia grisea (Cke.) Sacc.]. This map is the densest yet reported for this crop and will be a valuable resource for the pearl millet community.

Quantitative trait loci associated with soybean seed weight and composition under different phosphorus levels

“…Broad‐sense heritability ( H 2 ) was estimated for each trait using the procedure of Punnuri et al (). H 2 was defined as: where MSgen is the genotype mean square, MSrep is the replication mean square, and MSer is the error mean square from the two‐way ANOVA .…”

“…Broad-sense heritability (H 2 ) was estimated for each trait using the procedure of Punnuri et al (2016). H 2 was defined as:…”

High-resolution Linkage Map with Allele Dosage Allows the Identification of an Apomixis Region and Complex Traits in Guinea Grass (Megathyrsus maximus)

“…In addition, the use of a tetraploid genome, such as that of P. virgatum, may be more informative than the use of diploid genomes, considering our tetraploid mapping population, as there is a greater possibility of similar chromosomal rearrangements between these species (Daverdin et al, 2015). It is common to find a smaller number of SNPs in linkage maps of forage grass species without an assembled genome, as observed for common millet (Panicum miliaceum) (Rajput et al, 2016) and signalgrass (Urochloa decumbens) (Ferreira et al, 2019), than in those of species with a reference genome, such as foxtail millet (Setaria italica) (Jia et al, 2017) and pearl millet (Pennisetum glaucum) (Punnuri et al, 2016). Another alternative is the use of "pseudogenomes" assembled from GBS tags to include unique alleles of a species, as in Paspalum vaginatum, but the number of markers remained relatively small (Qi et al, 2019).…”

Genomics-assisted breeding in minor and pseudo-cereals

“…Studies involving the QTL mapping of other minor and pseudo-cereals, however, are relatively limited and mostly include studies in rye (Erath et al 2016, Miedaner et al 2018, Myśków et al 2018, Wang et al 2015, oat (Admassu-Yimer et al 2019, Babiker et al 2015, Pellizzaro et al 2016, Schneider et al 2015, Sunstrum et al 2018, Zimmer et al 2018, and millet. Of the various types of millet, pearl millet (Ambawat et al 2016, Aparna et al 2015, Kumar et al 2016b, 2018, Pucher et al 2018, Punnuri et al 2016, Taunk et al 2018 and foxtail millet (Fang et al 2016, Mauro-Herrera and Doust 2016, Ni et al 2017, Odonkor et al 2018, Wang et al 2017a, 2017b have received the majority of research attention, although one study also focused on proso millet (Rajput et al 2016). Notably, very few QTL mapping studies have focused on pseudocereals.…”