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

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 F 2:3 originating from the intraspecific cross NemX · SJ-2 were screened with 128 EcoR1/ Mse1 primer combinations. Putative AFLP markers were then screened with 60 F 2:7 RIL plants and four AFLP markers were found linked to rkn1. The linkage of AFLP markers to rkn1 was also confirmed in a F 2 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 F 2 (1R:3S), F 2:7 RIL (1R:1S) and the backcross population SJ-2 · F 1 (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 F 2:7 population. The PCRbased 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.

Identification of Molecular Markers Associated with Root‐Knot Nematode Resistance in Upland Cotton

“…Recently a few groups reported the development of molecular markers targeted to cotton RKN resistance using diff erent resistant germplasm (Bezawada et al, 2003;Shen et al, 2006;Wang and Roberts, 2006;Ynturi et al, 2006;Zhang et al, 2006b). Molecular markers closely associated with one or more nematode resistance genes could be used as reliable and accurate tools for RKN resistance screening, which may minimize the diffi culties associated with fi eld and greenhouse resistance phenotype evaluations.…”

“…Recently a few groups reported the development of molecular markers targeted to cotton RKN resistance using diff erent resistant germplasm (Bezawada et al, 2003;Shen et al, 2006;Wang and Roberts, 2006;Ynturi et al, 2006;Zhang et al, 2006b). The UBC693-420 and UBC781-964STS markers were mapped to the same linkage group with Mi 2 and several markers previously found linked with the RKN resistance gene rkn1 in Acala NemX Wang and Roberts, 2006), and RKN R gene or QTL in the Auburn resistance source (Shen et al, 2006;Ynturi et al, 2006), validating their potential usefulness in MAS for both the Auburn 634 RNR and Acala NemX resistance sources. The presence of multiple RKN resistance associated loci and polymorphic behavior of RKN associated markers among R breeding lines, such as the behavior of CIR316 and UCR-STS in Table 1, implies that additional molecular markers need to be identifi ed for effi cient application in a wide range of cotton germplasm.…”

“…Identifi cation of reliable molecular markers and confi rmation of their practical usefulness are highly desirable for RKN resistance research. Two SSR markers amplifi ed by primers BNL1231 and CIR316 and one cleaved amplifi ed polymorphic sequence (CAPS) marker (GHACC1) converted from an AFLP marker were found to be tightly linked to the resistance gene rkn1 in Acala NemX Wang and Roberts, 2006). One of the reasons could be that RKN resistance screening is not reliable on an individual plant basis (Zhang et al, 2006a).…”

“…In this population, 49 plants were classifi ed as resistant and 14 plants susceptible based on root-galling index. Considering that (i) Wild Mexico Jack Jones was also a race stock which may also contain gene Mi 1 ; (ii) Clevewilt and its derived line ST LA 887 contain a recessive R gene which may be allelic to rkn1 (Zhou, 1999;Bezawada et al, 2003); and (iii) the R gene is linked to the rkn1-associated markers (Shen et al, 2006;Wang and Roberts, 2006;Wang et al, 2006b;Ynturi et al, 2006; also see the following linkage analysis), we assign Mi 2 to the R gene detected by the segregation analysis. This indicated that there is at least one major R gene involved in the RKN resistance detected in the segregating population, although the population size did not preclude other minor genes contributing to the resistance.…”

Cotton Genomics

“…The heavy water use of cotton has drawn attention to molecular dissection of drought tolerance (Saranga et al 2001b(Saranga et al , 2004Zhao et al 2008). Disease resistance has also been a major focus, with published information for Verticillium (Bolek et al 2005;Wang et al 2008;Yang et al 2008), Xanthomonas Rungis et al 2002), Thielaviopsis (Niu et al 2008), and root knot nematode (Shen et al 2006a;Wang et al 2006b;Wang and Roberts 2006;Ynturi et al 2006;Niu et al 2007). Interest in hybrid cottons in some countries has drawn attention to a nuclear restorer of a cytoplasmic male sterility system (Guo et al 1998;Lan et al 1999;Zhang and Stewart 2004;Feng et al 2005;Wang et al 2007b).…”