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Development of AFLP and derived CAPS markers for root-knot nematode resistance in cotton

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Abstract

Resistance to root-knot nematode (Meloidogyne incognita) is determined by a single major gene rkn1 in Gossypium hirsutum Acala NemX cotton. Bulked segregant analysis (BSA) combined with amplified fragment length polymorphism (AFLP) was used to identify molecular markers linked to rkn1. DNA pools from homozygous susceptible (S) and resistant (R) bulks of an F2:3 originating from the intraspecific cross NemX × SJ-2 were screened with 128 EcoR1/Mse1 primer combinations. Putative AFLP markers were then screened with 60 F2:7 RIL plants and four AFLP markers were found linked to rkn1. The linkage of AFLP markers to rkn1 was also confirmed in a F2 population. The closest AFLP marker was converted to a cleaved amplified polymorphic sequence (CAPS) marker (designated GHACC1) by aligning the sequences from both susceptible and resistant parents. GHACC1 linkage to rkn1 was confirmed in the F2 (1R:3S), F2:7 RIL (1R:1S) and the backcross population SJ-2 × F1 (NemX × SJ-2) (1 heterozygous: 1 homozygous). The four AFLP markers, GHACC1 plus two SSR markers (CIR316 and BNL1231) linked to rkn1 from previous work were mapped to intervals of 2.6–14.2 cM from the rkn1 locus, and the genomic region around rkn1 was spanned to about 28.2 cM in the F2:7 population. The PCR-based GHACC1 and CIR316 markers were tested on 21 nematode resistant and susceptible cotton breeding lines and cultivars. GHACC1 was suitable for nematode resistance screening within G.␣hirsutum, but not G. barbadense, whereas CIR316 was useful in both species, indicating their␣potential for utilization in marker-assisted selection.

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Abbreviations

AFLP:

Amplified fragment length polymorphism

CAPS:

Cleaved amplified polymorphic sequence

MAS:

Marker-assisted selection

RIL:

Recombinant inbred line

STS:

Sequence tag site

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Acknowledgments

This study was funded in part by a Cooperative Research Agreement from Cotton Incorporated and a grant from the University of California Discovery Grant (BioSTAR) Program. The authors thank Steven Oakley, James Starr, California Planting Cotton Seed Distributors, and USDA Cotton Germplasm Center for providing cotton seed, Mikeal Roose for helpful advice, Mauricio Ulloa for providing SSR markers, and William Matthews, Teresa Mullens, Kathie Carter, Joe Kepiro and Xiangyang Shi for technical help.

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  1. Department of Nematology, University of California , Riverside, CA, 92521-0415, USA

    Congli Wang & Philip A. Roberts

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  1. Congli Wang
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  2. Philip A. Roberts
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Correspondence to Philip A. Roberts.

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Wang, C., Roberts, P.A. Development of AFLP and derived CAPS markers for root-knot nematode resistance in cotton. Euphytica 152, 185–196 (2006). https://doi.org/10.1007/s10681-006-9197-1

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