eprintid: 11728
rev_number: 11
eprint_status: archive
userid: 3170
dir: disk0/00/01/17/28
datestamp: 2021-03-08 15:18:19
lastmod: 2021-03-08 15:18:19
status_changed: 2021-03-08 15:18:19
type: article
metadata_visibility: show
creators_name: Allan, V
creators_name: Vetriventhan, M
creators_name: Senthil, R
creators_name: Geetha, S
creators_name: Deshpande, S
creators_name: Rathore, A
creators_name: Kumar, V
creators_name: Singh, P
creators_name: Reddymalla, S
creators_name: Azevedo, V C R
creators_gender: Female
creators_gender: Female
icrisatcreators_name: Vetriventhan, M
icrisatcreators_name: Senthil, R
icrisatcreators_name: Deshpande, S
icrisatcreators_name: Rathore, A
icrisatcreators_name: Kumar, V
icrisatcreators_name: Singh, P
icrisatcreators_name: Reddymalla, S
icrisatcreators_name: Azevedo, V C R
affiliation: Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University (TNAU), Coimbatore
affiliation: ICRISAT (Patancheru)
country: India
title: Genome-Wide DArTSeq Genotyping and Phenotypic Based Assessment of Within and Among Accessions Diversity and Effective Sample Size in the Diverse Sorghum, Pearl Millet, and Pigeonpea Landraces
ispublished: pub
subjects: S1.5.1
subjects: s1.2
subjects: s1.4
subjects: s2.13
divisions: Genebank
full_text_status: public
keywords: DArTseq, Within accession diversity, Effective population size, Landraces, Pearl millet, Pigeonpea, Regeneration, Sorghum
note: We thank Dr. Juan Andres (Biometrics and Statistics Unit
Head, CIMMYT, Mexico) for his kind help in AMOVA for
the DArTSeq data and Shannon diversity. Also, we extend
our thanks to Dr. Jorge Franco (Professor of Biometrics
and Statistics, Universidad de la República, Uruguay), Dr.
Carolina Paola Sansaloni (High-throughput genotyping and
sequencing specialist, CIMMYT, Mexico) and Dr. Fernando
Henrique Ribeiro (Associate Scientist-Agricultural Statistics,
CIMMYT, Mexico) for their kind support in calculation of
genotypic diversity.
abstract: Germplasm should be conserved in such a way that the genetic integrity of a given
accession is maintained. In most genebanks, landraces constitute a major portion of
collections, wherein the extent of genetic diversity within and among landraces of crops
vary depending on the extent of outcrossing and selection intensity infused by farmers.
In this study, we assessed the level of diversity within and among 108 diverse landraces
and wild accessions using both phenotypic and genotypic characterization. This included
36 accessions in each of sorghum, pearl millet, and pigeonpea, conserved at ICRISAT
genebank. We genotyped about 15 to 25 individuals within each accession, totaling
1,980 individuals using the DArTSeq approach. This resulted in 45,249, 19,052, and
8,211 high-quality single nucleotide polymorphisms (SNPs) in pearl millet, sorghum,
and pigeonpea, respectively. Sorghum had the lowest average phenotypic (0.090) and
genotypic (0.135) within accession distances, while pearl millet had the highest average
phenotypic (0.227) and genotypic (0.245) distances. Pigeonpea had an average of
0.203 phenotypic and 0.168 genotypic within accession distances. Analysis of molecular
variance also confirms the lowest variability within accessions of sorghum (26.3%)
and the highest of 80.2% in pearl millet, while an intermediate in pigeonpea (57.0%).
The effective sample size required to capture maximum variability and to retain rare
alleles while regeneration ranged from 47 to 101 for sorghum, 155 to 203 for pearl
millet, and 77 to 89 for pigeonpea accessions. This study will support genebank
curators, in understanding the dynamics of population within and among accessions,
in devising appropriate germplasm conservation strategies, and aid in their utilization for
crop improvement.
date: 2020-12
date_type: published
publication: Frontiers in Plant Science (TSI)
volume: 11
number: 587426
publisher: Frontiers Media
pagerange: 1-20
id_number: doi:10.3389/fpls.2020.587426
refereed: TRUE
issn: 1664-462X
official_url: https://doi.org/10.3389/fpls.2020.587426
related_url_url: https://scholar.google.com/scholar?hl=en&as_sdt=0%2C5&q=10.3389%2Ffpls.2020.587426&btnG=
related_url_type: pub
funders: Global Crop Diversity Trust (GCDT)
citation:   Allan, V and Vetriventhan, M and Senthil, R and Geetha, S and Deshpande, S and Rathore, A and Kumar, V and Singh, P and Reddymalla, S and Azevedo, V C R  (2020) Genome-Wide DArTSeq Genotyping and Phenotypic Based Assessment of Within and Among Accessions Diversity and Effective Sample Size in the Diverse Sorghum, Pearl Millet, and Pigeonpea Landraces.  Frontiers in Plant Science (TSI), 11 (587426).  pp. 1-20.  ISSN 1664-462X     
document_url: http://oar.icrisat.org/11728/1/fpls-11-587426.pdf