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Association mapping to discover significant marker-trait associations for resistance against fusarium wilt variant 2 in pigeonpea [Cajanus cajan (L.) Millspaugh] using SSR markers

  • Plant Genetics • Original Paper
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Abstract

Pigeonpea production is severely constrained by wilt disease caused by Fusarium udum. In the current study, we discover the putative genomic regions that control resistance response to variant 2 of fusarium wilt using association mapping approach. The association panel comprised of 89 diverse pigeonpea genotypes including seven varieties, three landraces and 79 germplasm lines. The panel was screened rigorously for 3 consecutive years (2013–14, 2014–15 and 2015–2016) against variant 2 in a wilt-sick field. A total of 65 pigeonpea specific hypervariable SSR markers (HASSRs) were screened representing seven linkage groups and 29 scaffolds of the pigeonpea genome. A total of 181 alleles were detected, with average values of gene diversity and polymorphism information content (PIC) of 0.55 and 0.47, respectively. Further analysis using model based (STRUCTURE) and distance based (clustering) approaches separated the entire pigeonpea collection into two distinct subgroups (K = 2). The marker trait associations (MTAs) were established based on three-year wilt incidence data and SSR dataset using a unified mixed linear model. Consequently, six SSR markers were identified, which were significantly associated with wilt resistance and explained up to 6% phenotypic variance (PV) across the years. Among these SSRs, HASSR18 was found to be the most stable and significant, accounting for 5–6% PV across the years. To the best of our knowledge, this is the first report of identification of favourable alleles for resistance to variant 2 of Fusarium udum in pigeonpea using association mapping. The SSR markers identified here will greatly facilitate marker assisted resistance breeding against fusarium wilt in pigeonpea.

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Acknowledgements

This work was financially supported by the Indian Council of Agricultural Research-Network Project on Transgenic in Crops- Sub Project- Functional Genomics in Pigeonpea.

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Authors and Affiliations

  1. Plant Biotechnology, Indian Institute of Pulses Research, Kanpur, 208 024, India

    Prakash G. Patil, Alok Das & Meenal Rathore

  2. Biotechnology, Indian Institute of Pulses Research, Kanpur, 208 024, India

    Jyotirmay Dubey

  3. Plant breeding, Indian Institute of Pulses Research, Kanpur, 208 024, India

    Abhishek Bohra

  4. Plant Pathology, Indian Institute of Pulses Research, Kanpur, 208 024, India

    R. K. Mishra & P. R. Saabale

  5. Division of Plant Biotechnology, Indian Institute of Pulses Research, Kanpur, 208 024, India

    N. P. Singh

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  1. Prakash G. Patil
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Correspondence to Prakash G. Patil.

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Communicated by: Barbara Naganowska

Electronic supplementary material

Suppl. Fig. 1

Representative partial map showing genome positions of markers associated with resistance to wilt (indicated with arrow). SSR markers were located on the reference genome using the BLAT options of genome browser in Legume information system. The marker Mb positions were converted and represented in cM map units and map was drawn with GGT software (Van-Berloo 2008) (GIF 5812 kb)

High resolution image (TIFF 3000 kb)

Suppl. Fig. 2

Weather graph depicting differences for temperature, relative humidity and rainfall for three cropping seasons (July–April) (Major differences were indicated by circle in the graph) (GIF 6094 kb)

High resolution image (TIFF 6632 kb)

Suppl. Table 1

Phenotypic data on percent wilt incidence for 89 pigeonpea genotypes for 3 years (DOC 106 kb)

Suppl. Table 2

Phenotypic effects of major marker allele at six significantly associated SSR locus against FW (DOC 36 kb)

Suppl. Table 3

Comparison of weather data for the 4 months (November to December for each year) during which phenotyping against FW was carried out (DOC 35 kb)

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Patil, P.G., Dubey, J., Bohra, A. et al. Association mapping to discover significant marker-trait associations for resistance against fusarium wilt variant 2 in pigeonpea [Cajanus cajan (L.) Millspaugh] using SSR markers. J Appl Genetics 58, 307–319 (2017). https://doi.org/10.1007/s13353-017-0400-y

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