New Hypervariable SSR Markers for Diversity Analysis, Hybrid Purity Testing and Trait Mapping in Pigeonpea [Cajanus cajan (L.) Millspaugh]

Publication Overview
TitleNew Hypervariable SSR Markers for Diversity Analysis, Hybrid Purity Testing and Trait Mapping in Pigeonpea [Cajanus cajan (L.) Millspaugh]
AuthorsBohra A, Jha R, Pandey G, Patil PG, Saxena RK, Singh IP, Singh D, Mishra RK, Mishra A, Singh F, Varshney RK, Singh NP
TypeJournal Article
Journal NameFrontiers in plant science
Volume8
Year2017
Page(s)377
CitationBohra A, Jha R, Pandey G, Patil PG, Saxena RK, Singh IP, Singh D, Mishra RK, Mishra A, Singh F, Varshney RK, Singh NP. New Hypervariable SSR Markers for Diversity Analysis, Hybrid Purity Testing and Trait Mapping in Pigeonpea [Cajanus cajan (L.) Millspaugh]. Frontiers in plant science. 2017; 8:377.

Abstract

Draft genome sequence in pigeonpea offers unprecedented opportunities for genomics assisted crop improvement via enabling access to genome-wide genetic markers. In the present study, 421 hypervariable simple sequence repeat (SSR) markers from the pigeonpea genome were screened on a panel of eight pigeonpea genotypes yielding marker validation and polymorphism percentages of 95.24 and 54.11%, respectively. The SSR marker assay uncovered a total of 570 alleles with three as an average number of alleles per marker. Similarly, the mean values for gene diversity and PIC were 0.44 and 0.37, respectively. The number of polymorphic markers ranged from 39 to 89 for different parental combinations. Further, 60 of these SSRs were assayed on 94 genotypes, and model based clustering using STRUCTURE resulted in the identification of the two subpopulations (K = 2). This remained in close agreement with the clustering patterns inferred from genetic distance (GD)-based approaches i.e., dendrogram, factorial and principal coordinate analysis (PCoA). The AMOVA accounted majority of the genetic variation within groups (89%) in comparison to the variation existing between the groups (11%). A subset of these markers was implicated for hybrid purity testing. We also demonstrated utility of these SSR markers in trait mapping through association and bi-parental linkage analyses. The general linear (GLM) and mixed linear (MLM) models both detected a single SSR marker (CcGM03681) with R2 = 16.4 as associated with the resistance to Fusarium wilt variant 2. Similarly, by using SSR data in a segregating backcross population, the corresponding restorer-of-fertility (Rf) locus was putatively mapped at 39 cM with the marker CcGM08896. However, The marker-trait associations (MTAs) detected here represent a very preliminary type and hence demand deeper investigations for conclusive evidence. Given their ability to reveal polymorphism in simple agarose gels, the hypervariable SSRs are valuable genomic resource for pigeonpea research community, particularly in South Asia and East Africa where pigeonpea is primarily grown.
Stocks
This publication contains information about 3 stocks:
Stock NameUniquenameType
ICPL_88039AICPL_88039Abreeding_research_material
AK_250189RAK_250189Rbreeding_research_material
ICPL_88039A/AK_250189R-BCICPL_88039A/AK_250189R-BCpopulation
Features
This publication contains information about 23 features:
Feature NameUniquenameType
CcM01841CcM01841genetic_marker
CcM02751CcM02751genetic_marker
CcM02855CcM02855genetic_marker
CZ681938CZ681938genetic_marker
HA-SSR0110HA-SSR0110genetic_marker
HA-SSR0120HA-SSR0120genetic_marker
HA-SSR0190HA-SSR0190genetic_marker
HA-SSR0194HA-SSR0194genetic_marker
HA-SSR0199HA-SSR0199genetic_marker
HA-SSR0201HA-SSR0201genetic_marker
HA-SSR0202HA-SSR0202genetic_marker
HA-SSR0205HA-SSR0205genetic_marker
HA-SSR0284HA-SSR0284genetic_marker
HA-SSR0295HA-SSR0295genetic_marker
HA-SSR0003HA-SSR0003genetic_marker
HA-SSR0046HA-SSR0046genetic_marker
HA-SSR0005HA-SSR0005genetic_marker
HA-SSR0057HA-SSR0057genetic_marker
HA-SSR0006HA-SSR0006genetic_marker
HA-SSR0072HA-SSR0072genetic_marker
HA-SSR0081HA-SSR0081genetic_marker
HA-SSR0092HA-SSR0092genetic_marker
Restorer of fertilityRestorer of fertility-Rfheritable_phenotypic_marker
Featuremaps
This publication contains information about 1 maps:
Map Name
Pigeon_pea-ICPL_88039A/AK_250189R-BC
Properties
Additional details for this publication include:
Property NameValue
LanguageEnglish
Journal CountrySwitzerland
ISSN1664-462X
Language Abbreng
Publication ModelElectronic-eCollection
DOI10.3389/fpls.2017.00377
Journal AbbreviationFront Plant Sci
Publication Date2017
Publication TypeJournal Article
pISSN1664-462X
Elocation10.3389/fpls.2017.00377
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DatabaseAccession
PMID: PubMedPMID:28408910