eprintid: 11764
rev_number: 10
eprint_status: archive
userid: 3170
dir: disk0/00/01/17/64
datestamp: 2021-03-26 03:51:55
lastmod: 2021-03-26 03:53:41
status_changed: 2021-03-26 03:51:55
type: article
metadata_visibility: show
creators_name: Kanfany, G
creators_name: Serba, D D
creators_name: Rhodes, D
creators_name: St. Amand, P
creators_name: Bernardo, A
creators_name: Gangashetty, P I
creators_name: Kane, N A
creators_name: Bai, G
icrisatcreators_name: Gangashetty, P I
affiliation: Institut Sénégalais de Recherches Agricoles (ISRA), Centre National de Recherches Agronomiques de Bambey, Diourbel, Senegal
affiliation: Agricultural Research Center-Hays, Kansas State University, USA
affiliation: Department of Agronomy, Kansas State University, Manhattan,
affiliation: Hard Winter Wheat Genetics Research Unit, USDA-ARS, Manhattan,
affiliation: ICRISAT (Niamey)
affiliation: Institut Sénégalais de Recherches Agricoles/Centre d’Étude Régional pour l’Amélioration de l’Adaptation à la Sécheresse (ISRA/ CERAAS), Thiès, Senegal
country: Senegal
country: USA
title: Genomic diversity in pearl millet inbred lines derived from landraces and improved varieties
ispublished: pub
subjects: PLB1
subjects: S1.5.1
subjects: s2.13
divisions: CRPS1
full_text_status: public
keywords: Genetic diversity, Population structure, Pennisetum glaucum, Cenchrus americanus, Genotyping-bysequencing,
SNPs, Linkage disequilibrium
note: Mention of trade names or commercial products in this publication is solely
for the purpose of providing specific information and does not imply
recommendation or endorsement by any part herein. This is contribution
number 20-185-J from the Kansas Agricultural Experiment Station.
abstract: Background: Genetic improvement of pearl millet is lagging behind most of the major crops. Development of
genomic resources is expected to expedite breeding for improved agronomic traits, stress tolerance, yield, and
nutritional quality. Genotyping a breeding population with high throughput markers enables exploration of genetic
diversity, population structure, and linkage disequilibrium (LD) which are important preludes for marker-trait
association studies and application of genomic-assisted breeding.
Results: Genotyping-by-sequencing (GBS) libraries of 309 inbred lines derived from landraces and improved
varieties from Africa and India generated 54,770 high quality single nucleotide polymorphism (SNP) markers. On
average one SNP per 29 Kb was mapped in the reference genome, with the telomeric regions more densely
mapped than the pericentromeric regions of the chromosomes. Population structure analysis using 30,208 SNPs
evenly distributed in the genome divided 309 accessions into five subpopulations with different levels of admixture.
Pairwise genetic distance (GD) between accessions varied from 0.09 to 0.33 with the average distance of 0.28. Rapid
LD decay implied low tendency of markers inherited together. Genetic differentiation estimates were the highest
between subgroups 4 and 5, and the lowest between subgroups 1 and 2.
Conclusions: Population genomic analysis of pearl millet inbred lines derived from diverse geographic and
agroecological features identified five subgroups mostly following pedigree differences with different levels of
admixture. It also revealed the prevalence of high genetic diversity in pearl millet, which is very useful in defining
heterotic groups for hybrid breeding, trait mapping, and holds promise for improving pearl millet for yield and
nutritional quality. The short LD decay observed suggests an absence of persistent haplotype blocks in pearl millet. The
diverse genetic background of these lines and their low LD make this set of germplasm useful for traits mapping.
date: 2020-07
date_type: published
publication: BMC Genomics (TSI)
volume: 21
number: 1
publisher: BMC
pagerange: 1-12
id_number: doi:10.1186/s12864-020-06796-4
refereed: TRUE
issn: 1471-2164
official_url: https://doi.org/10.1186/s12864-020-06796-4
related_url_url: https://scholar.google.com/scholar?hl=en&as_sdt=0%2C5&q=10.1186%2Fs12864-020-06796-4&btnG=
related_url_type: pub
funders: United States Department of Agriculture Foreign Agricultural Service
citation:   Kanfany, G and Serba, D D and Rhodes, D and St. Amand, P and Bernardo, A and Gangashetty, P I and Kane, N A and Bai, G  (2020) Genomic diversity in pearl millet inbred lines derived from landraces and improved varieties.  BMC Genomics (TSI), 21 (1).  pp. 1-12.  ISSN 1471-2164     
document_url: http://oar.icrisat.org/11764/1/s12864-020-06796-4.pdf