Molecular and phenotypic analyses of genetic variation in avocado (Persea americana Mill.)

I present a study of genetic variation in avocado using both molecular and phenotypic approaches. In chapter two I sequenced four nuclear gene loci to investigate levels of nucleotide polymorphism and linkage disequilibrium in a sample of 21 wild avocado accessions and 33 cultivars. Results show that although avocado is an outcrossing tree, the overall level of genetic variation is not exceptionally high compared to other plant species. Linkage disequilibrium decays to half of its original value within 500 bp in both wild and cultivated samples; recombination rates are moderate and also similar in both wild and cultivated groups. Significant genetic differentiation was found in three wild avocado geographic groups. Cluster analysis assigned 33 cultivars into three populations: "Central Mexican". "Southern Mexican/Guatemalan" and "West Indian" and one hybrid group, mostly composed of "Mexican by Guatemalan".; In chapter three I demonstrate a method in which allele-specific PCR (AS-PCR) and computational phasing tools are combined for relatively high-throughput, efficient resolution of phase in resequencing studies. Using data from multiple loci of avocado that were fully experimentally phased, we demonstrate that popular computational tools (PHASE) can accurately phase heterozygous individuals with common SNPs and/or common haplotypes. However, we also demonstrate that experimental phasing using AS-PCR can efficiently supplement computational phasing, providing a rapid means to phase individuals with rare SNPs or haplotypes and with heterozygous indel polymorphisms. By following simple stepwise procedures, this method can result in more efficient and accurate experimental phasing of haplotypes in population genetic data collections.; In chapter four, I analyze a multi-year quantitative genetics experiment using progeny of cultivar 'Gwen' (maternal parent). The results show that broad-sense heritability (H2) is moderate for tree growth rates, flowering abundance and fruit set. The H2 value is somewhat lower than expected but within the range of breeding potential. I also found a moderate correlation between tree growth rate and fruit load, and none between growth rate and flower abundance. Different pollen donors have different impacts on tree growth rates, flower abundance and fruit set.