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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #358214

Research Project: Improving Crop Efficiency Using Genomic Diversity and Computational Modeling

Location: Plant, Soil and Nutrition Research

Title: Development of a high-density linkage map and tagging leaf spot resistance in pearl millet uysing genotyping-by-sequencing markers

item PUNNURI, SOMASHEKHAR - Fort Valley State University
item WALLACE, JASON - University Of Georgia
item Knoll, Joseph - Joe
item HYMA, KATIE - Cornell University
item MITCHELL, SHARON - Cornell University
item Buckler, Edward - Ed
item VARSHNEY, RAJEEV - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item SINGH, BHARAT - Fort Valley State University

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/29/2016
Publication Date: 5/6/2016
Citation: Punnuri, S.M., Wallace, J.G., Knoll, J.E., Hyma, K.E., Mitchell, S.E., Buckler IV, E.S., Varshney, R.K., Singh, B.P. 2016. Development of a high-density linkage map and tagging leaf spot resistance in pearl millet uysing genotyping-by-sequencing markers. The Plant Genome. 9(2):1-13.

Interpretive Summary: Pearl millet is a key food security crop in much of the developing world as it is quite tolerant to heat, drought, and soil toxicity. It also has higher water and nitrogen-use efficiency than most other cereals, and will thrive where other crops would not be able to survive. In the United States, the demand for pearl millet has risen because of the need for gluten-free flour options and less-expensive livestock feed. Even though the crop has great adaptations to stressful environments, the genomic resources attached are lacking compared to most other cereal crops. This study created a high-density genetic map that could be a resource for future study of pearl millet. This genetic map will facilitate the identification of key genes relevant to yield, adaptation, and quality. It can also be used in genomic selection to accelerate breeding.

Technical 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-by-sequencing (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 99D2B1’ and ‘Tift 454’. DNA from 186 RILs, the parents, and the F1 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.