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ARS Home » Southeast Area » Tifton, Georgia » Crop Genetics and Breeding Research » Research » Publications at this Location » Publication #402054
Research Project: Genetic Improvement and Cropping Systems of Warm-season Grasses for Forage, Feedstocks, Syrup, and Turf

Location: Crop Genetics and Breeding Research

Title: High-density genotyping for pearl millet linkage map improvement with next-generation sequencing data

Author
item PUNNURI, SOMASHEKHAR - Fort Valley State University
item WALLACE, JASON - University Of Georgia
item Knoll, Joseph - Joe

Submitted to: Book Chapter
Publication Type: Book / Chapter
Publication Acceptance Date: 6/11/2024
Publication Date: 8/21/2024
Citation: Punnuri, S.M., Wallace, J.G., Knoll, J.E. 2024. High-density genotyping for pearl millet linkage map improvement with next-generation sequencing data. In: Srivastava, R.K., Satyavathi, C.T., Varshney, R.K. (eds) The Pearl Millet Genome. Compendium of Plant Genomes. Springer, Cham. pp. 97-105. https://doi.org/10.1007/978-3-031-56976-0?7.
DOI: https://doi.org/10.1007/978-3-031-56976-0?7

Interpretive Summary: Pearl millet is a hardy, drought tolerant and climate-smart crop that performs well even in extreme temperatures. Until recently it was considered an orphan crop with poor genomic resources, but recent next-generation sequencing (NGS) technologies have moved it into the modern genomics era. This chapter discusses how the new NGS technologies have been applied to improve genetic mapping in this important, but formerly neglected, crop. We used our own published genetic map of pearl millet, developed from 16,650 Genotyping by Sequencing (GBS) markers, and compared with other published maps. We report that this map contained the highest density of markers compared to other maps. The pearl millet plant population used for linkage map construction was also evaluated for several agronomic and physiological traits. Analysis revealed that high density genotyping increases the resolution of genetic map confidence intervals identified for the traits. In summary, these results reveal that NGS studies play a prominent role in improving linkage map saturation and its utility in breeding programs. The information gained from this study can further enhance breeding programs through marker-assisted selection and genomic selection.

Technical Abstract: Pearl millet [Pennisetum glaucum (L.) R. Br; also Cenchrus americanus (L.) Morrone] is a hardy, drought tolerant and climate-smart crop that performs well even in extreme temperatures. Until recently it was considered an orphan crop with poor genomic resources, but recent next-generation sequencing (NGS) technologies have moved it into the modern genomics era. There are several maps in pearl millet containing different types of markers. We used our own published genetic map developed from 16,650 Genotyping by Sequencing (GBS) markers and compared with other published maps. The map was used to confirm the collinearity of markers against a consensus map. We report that this map contained the highest density of markers per cM compared to other maps. The order of markers and orientation of chromosomes remained the same for the majority of regions. The recombinant inbred line (RIL) population used for linkage map construction was also evaluated for several agronomic and physiological traits. Quantitative trait locus (QTL) analysis revealed that high density genotyping increases the resolution of genetic map confidence intervals identified for the traits. In summary, these results reveal that NGS studies play a prominent role in improving linkage map saturation and its utility in breeding programs. The information gained from this study can further enhance breeding programs through marker-assisted selection and genomic selection.