Studies on QTL analysis for growth characteristics in apple (Malus X domestica Borkh.)
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Date
2014
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Publisher
YSPU
Abstract
The present investigation on apple was carried out to map QTL for two vegetative characteristics,
vegetative bud break and crotch angle. Along with QTL mapping, the study also aimed at developing EST-SSR markers for apple and to study genetic diversity among a collection of 48 apple genotypes.
In silico analysis of 330181 EST sequences of apple was carried and SSR motifs were analysed among
the sequences after assembly by removing redundancy. 4570 sequences were found to contain SSR motifs. 25 sequences were selected for primer designing. Functional domain analysis and sequence annotation was done for the selected 25 sequences. Genetic diversity was estimated in collection of 48 apple genotypes, comprising of commercial varieties, wild relatives and rootstocks, using 25 EST-SSR, 25 genomic SSR and 38 ISSR primers. Results were analyzed in the form of dendrograms, similarity matrices and polymorphism information content. Highest polymorphism of 97.81% was revealed by ISSR primers. Dendrograms clustered the genotypes according to their origin, with a few exceptions. For QTL analysis, cultivars ‘Red Delicious’ and ‘Maharaji’ were used as parents. F1 population was raised by crossing the parental plants and was used as mapping population. Parental polymorphism survey carried out using 164 SSR primers, both genomic and EST derived, revealed 97 polymorphic primers. These 97 primers were used for genotyping the mapping population of 120 plants. The individuals of the mapping population as well as the parental plants were scored for the two phenotypic traits under consideration. A linkage map consisting of 74 markers grouped into four linkage groups and covering 971.6 cM was generated using MAPMAKER/EXP ver 3.0b. The first linkage group was the largest spanning 754.4cM with 55 markers. The second contained 2 markers in a distance of 14.7cM. The third linkage group spanned 149.7 cM containing 12 markers and the fourth linkage group contained 5markers with a length of 52.8 cM. QTL analysis was carried out using QTL Cartographer. Two significant QTL for bud burst were identified, one on chromosome 1 between markers P26 and P32, responsible for 7.4% of the phenotypic variance and other on chromosome 3 between markers P40 and P15, responsible7.9% of the phenotypic variance. QTL Six significant QTL for crotch angle were detected on chromosome 1, located between markers P26 and P32; P7 and P25; CH01A07b and CH01C06; CH01F02 and CH02A04; IISRS12 and E13 and IISRS9 and MS06G03, and responsible for 34% , 23.2%, 48% , 40.9% , 48.2% and 12% of the phenotypic variation, respectively. Seventh QTL for crotch angle was located on chromosome 3 between P16 and CH02F06 and was responsible for 6.7% of the phenotypic variation.
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Keywords
apples, genetics, genotypes, polymorphism, genomes, planting, dna, fruits, genetic structures, chromosome mapping