Development of SCAR/CAPS marker
The amplification of DNA of parental lines JG-62 (susceptible) and WR-315 (resistant) using five different
SCAR primer sets produced monomorphic bands. The SCAR primer A07CSCAR-3 producing single, specific predicted size in both susceptible (JG62) and resistant parent (WR315) was selected and amplified products from both parental lines were sequenced. Comparison of consensus sequence information of SCAR amplified products from both the parental lines JG-62 and WR-315 enabled the identification of single nucleotide polymorphism (SNP) with a restriction site mutation for restriction enzyme
Aci I (C▼CGC/GGC▲G) specific to resistant parent WR-315 at 219 bp (Fig 2), which clearly distinguished the susceptible and resistant parents. The restriction enzyme digestion of monomorphic SCAR product from both the parents JG-62 and WR-315 produced an expected electrophoretic banding pattern of two bands of size 212 bp and 159 bp in resistant parent WR-315 and single band of 371 bp in susceptible parent JG-62 (Fig 3).
The essential requirement of any MAS programme involves the identification of polymorphic markers that are closely linked to trait of interest and their validation. RAPD markers are the first generation marker system extensively used for germplasm classification in addition to their usefullness in gene tagging and mapping studies owing to their major attributes such as use of universal primers, short period with cost effectiveness, requirement small quantity of DNA for analysis and also non requirement of cloned DNA probes and hybridization filters
(Ranade et al., 2001). Although, RAPD markers provide an efficient assay for polymorphism as the differences in amplicon primarily results from the differences in their priming site or amplifying DNA segment from one parent but not in the other and used successfully to map chickpea wilt resistance loci
(Soregaon et al., 2007 and
Babayeva et al., 2018), the technique is dominant and sensitive to modification in PCR reaction condition, eventually resulting in poor reproducibility. These limitations has led to the successful conversion of RAPD marker linked to different traits into allele-specific or locus-specific primers (SCAR/CAPS) and it has been reported in melon, tomato, faba bean, black gram and mung been by
Zheng et al., (1999); Zhang and John (2001);
Gutierrz et al. (2006);
Prashanti et al. (2011);
Dhole and Reddy (2013) respectively.
Segregation and linkage analysis of CAPS marker
The c
2 test for monogenic inheritance of CAPS marker and wilt reaction displayed an expected 1:1 segregation ratio in RILs population. Among 117 RILs, 61 RILs produced CAPS banding pattern similar to WR-315. The digenic analysis of wilt reaction and marker was carried out to determine the linkage between markers and wilt resistance. The joint segregation of CAPS marker together with 60
th day wilt reaction in all the three seasons indicated significant deviation from 1:1:1:1 ratio in the RILs suggesting linkage between CAPS marker and wilt reaction (Table 2). Further in an effort to map the CAPS marker on to the sequence based physical map of chickpea by
in silico approach using BLAST search tool of NCBI showed significant similarity with LOC101491241 on chromosome Ca4 (E-value = 0.0) of the chickpea genome with a putative function of wound responsive family protein determined using chickpea transcriptome database.
The first DNA markers linked to the
Fusarium wilt race 1A at H
1 locus was identified by
Mayer et al., (1997) using allele specific associated primer (ASAP) CS27
700. Similarly, RAPD marker A07C
417 linked to H
2 locus have been identified by
Soregaon et al., (2007). Both of these allele specific markers were developed in different genetic backgrounds segregating independently for each locus. Independent segregation of markers linked to H
1 (CS27
700) and H
2 (A07C
417) locus were also confirmed using RILs of cross JG-62 x WR-315 revealing reliability of both these DNA markers (
Brinda and Ravikumar, 2005;
Soregaon and Ravikumar, 2010). Along with these linked markers, many SSR markers linked to wilt resistance have been identified by several researchers
(Radhika et al., 2007; Gowda et al., 2009; Patil et al., 2014 and
href="#jingade_2015">Jingadae et al., 2015). However, many of these markers need to be validated in different genetic background for their association with wilt resistance and it is also necessary to develop high density of polymorphic markers in these region, which will enable fine mapping of resistance locus (
MPerez-de-Castro et al., 2012). Hence, identifying markers tightly linked to resistance loci/QTL will provide an effective solution for resistance deployment via MAS particulary in case of complex inheritance pattern of disease resistance.
In the present investigation, SNP has been identified in the monomorphic SCAR locus of RAPD primer A07C
417, which is able to differentiate between susceptible and resistant genotypes enabling the development of reproducible codominant CAPS marker. The mapping population (RILs) used were developed by hybridization of highly susceptible (JG62) and resistant parent (WR315) segregating independently for both H
1 and H
2 locus potentially generating a full range of variability for wilt resistance. Further, to overcome the problems associated with disease screening of segregating population in wilt sick plots, development of standardized disease screening using uniform wilt sick pots in green house enabled efficient screening of segregating population. Disease screening of RILs for wilt reaction in wilt sick pots and wilt sick plots enabled detection of linkage association of CAPS marker with H
2 locus of
Fusarium wilt resistance. Thus, identification of SNP and the development of codominant CAPS marker in this study may find its usefulness in precise genetic mapping and marker assisted trait introgression of resistance locus into elite cultivar.