Genetic analysis of reproductive and nut traits in almond [Prunus dulcis (Mill.) D.A. Webb]

Abstract

Almond is a perennial tree crop with a gametophytic self-incompatibility (SI) system. The SI system of almond is controlled by a multi-allelic locus, S, which is about 70,000 bp long. A nearly complete sequence for the entire S locus sequence has been available only for the S₇ haplotype. In this research, next-generation sequencing technology was implemented to sequence the entire S locus simultaneously from 15 haplotypes. The results confirmed the accuracy of available S₇ haplotype sequence, generated the entire S locus sequences for the Sf [f subscript], S₁ and S₈ haplotypes and generated partial S locus sequences for 11 other haplotypes (S₃, S₅, S₆, S₉, S₁₃, S₁₄, S₁₉, S₂₂, S₂₃, S₂₅ and S₂₇). Comparisons among haplotype sequences revealed higher polymorphism in the region where the S-RNase and SFB genes are located and considerable differences in the number and locations of long terminal repeat retrotransposons. There are about 50 known S alleles, of which one confers self-fertility. For some of these, complete or partial S-RNase and SFB sequences are available. Here, more complete sequences were generated for several alleles of the S-RNase gene (S₃, S₆, S₉, S₁₃, S₁₉, S₂₂ and S₂₅) and the SFB gene (S₉, S₂₃ and S₂₇). In almond breeding, SI limits the parental combinations that can be used for crossing. Detection of S alleles prior to crossing would be beneficial. Until now, molecular detection of the S alleles has relied on detection of length polymorphisms in the S-RNase gene. Here, single nucleotide polymorphisms (SNPs) in the S-RNase and SFB genes were used in designing assays to distinguish among S alleles. This thesis also reports on the construction of linkage maps for Nonpareil and Lauranne based on genotyping-by-sequencing (GBS) and on the design of uniplex assays for detection of SNPs detected by GBS. These assays were applied to additional Nonpareil × Lauranne progeny and to progeny from three other Nonpareil crosses (Nonpareil × Constantί, Nonpareil × Tarraco and Nonpareil × Vairo). Data from all four populations were used to generate a composite map for Nonpareil. Comparisons of marker positions detected for Nonpareil and Lauranne with positions in the peach genome confirmed high collinearity between the almond and peach genomes. Quantitative trait loci analysis detected 23 genomic regions as affecting nut and/or kernel traits in Nonpareil × Lauranne. Nine and 14 QTLs were detected for Nonpareil and Lauranne, respectively. Of the kernel and nut traits mapped here, shell weight, kernel shape, tocopherol concentration, fatty acid concentration and oleic/linoleic ratio were mapped for the first time in almond. For shell hardness and oleic/linoleic ratio, markers were identified that could be useful for marker-assisted selection. Some of the QTLs related to fatty acid and tocopherol concentration were closely located to the genes that are known to be involved in the synthesis of fatty acids and/or tocopherols. Some of the sequence information generated here may be useful for designing primers to amplify these genes (or components of these genes) for resequencing from multiple almond genotypes.