A high-density linkage map construction in guava (Psidium guajava L.) using genotyping by sequencing and identification of QTLs for leaf, peel, and pulp color in an intervarietal mapping population.

Psidium guajava L. is an important fruit crop in the tropical and subtropical regions of the world. The advanced breeding methods are not employed for important commercial traits like peel and pulp color, seed hardiness, fruit size, etc., due to the scarcity of genome-wide molecular markers and high-density linkage maps. In this study, we employed single-nucleotide polymorphism (SNP) markers and identified quantitative trait loci (QTL) regions that are associated with color traits of leaf, peel, and pulp in the guava intervarietal mapping population. The mapping population was developed from the contrasting genotypes of fruit and leaf color. Variations in color among the segregating hybrids were recorded both visually and using a Color reader. A high-density linkage map of guava was constructed using the SNP markers from genotyping by sequencing (GBS) of 150 hybrid individuals of the cross 'Arka Poorna' (green) x 'Purple Local' (purple). The integrated linkage map consisted of 1426 SNPs mapped on 11 linkage groups (LG), spanning a total distance of around 730 cM with an average of 129.6 markers per LG. Through QTL analysis for color traits, a minor QTL region was identified for visually scored leaf color and peel color on LG1, whereas a major QTL was detected for pulp color in LG4. The Hunter color values (L* and, a*) also had major QTLs with overlapping marker intervals for leaf and peel colors, establishing the association of SNP markers to the trait. The QTLs harbored genes and transcription factors involved in lycopene and anthocyanin pigment biosynthesis. This is the first report of a high-density linkage map based on SNP markers in guava and QTL mapping for color characters in leaf, fruit peel and pulp. The genotyping information generated in this study can aid in genetic engineering and marker-assisted breeding in guava.

Development of new microsatellite markers from Mango (Mangifera indica) and cross-species amplification.

PREMISE OF THE STUDY: Microsatellite markers were developed and characterized to assess the genetic diversity among mango (Mangifera indica) cultivars and to test their amplification in closely related species. METHODS AND RESULTS: Thirty-six microsatellite (simple sequence repeats; SSR) loci were isolated by a microsatellite-enriched partial genomic library method. Primers designed for these loci were characterized using 30 diverse mango cultivars. The number of alleles ranged from 3 to 19 with an average of 9.2 alleles per locus. Polymorphic information content values ranged from 0.185 to 0.920 with a mean of 0.687. The total value for the probability of identity was 2.42 × 10(-31). CONCLUSIONS: The newly identified SSRs would be useful in genetic diversity studies, finger-printing, and mapping. Loci from five related species, M. odorata, M. anadamanica, M. zeylanica, M. camptosperma, and M. griffithii, were successfully amplified using these SSR primers, showing their potential utility across species.