Quantitative Trait Locus Analysis in Avocado: The Challenge of a Slow-maturing Horticultural Tree Crop

Abstract

<jats:p>The glossy, green-fleshed fruit of the avocado (<jats:italic>Persea americana</jats:italic>) has been the object of human selection for thousands of years. Recent interest in healthy nutrition has singled out the avocado as an excellent source of several phytonutrients. Yet as a sizeable, slow-maturing tree crop, it has been largely neglected by genetic studies, owing to a long breeding cycle and costly field trials. We use a small, replicated experimental population of 50 progeny, grown at two locations in two successive years, to explore the feasibility of developing a dense genetic linkage map and to implement quantitative trait locus (QTL) analysis for seven phenotypic traits. Additionally, we test the utility of candidate-gene single-nucleotide polymorphisms developed to genes from biosynthetic pathways of phytonutrients beneficial to human health. The resulting linkage map consisted of 1346 markers (1044.7 cM) distributed across 12 linkage groups. Numerous markers on Linkage Group 10 were associated with a QTL for flowering type. One marker on Linkage Group 1 tracked a QTL for β-sitosterol content of the fruit. A region on Linkage Group 3 tracked vitamin E (α-tocopherol) content of the fruit, and several markers were stable across both locations and study years. We argue that the pursuit of linkage mapping and QTL analysis is worthwhile, even when population size is small.</jats:p>

Insights into the domestication of avocado and potential genetic contributors to heterodichogamy

“…To improve contiguity, we anchored and scaffolded the C + H assembly using a published genetic map, based on a cross between Gwen and Fuerte ( Ashworth et al 2019 ). This exercise resulted in 12 scaffolds that were assigned to 12 linkage groups, along with unplaced contigs.…”

“…HapSolo v0.1 ( Solares et al 2021 ), which identifies and removes alternative haplotypes, was then run on the assembly with default parameters and 50,000 iterations, producing the Canu + Hapsolo (C + H) assembly. Scaffolding was based on a Gwen × Fuerte genetic map ( Ashworth et al 2019 ) by aligning the C + H assembly using NCBI BLAST v2.2.31+ ( Altschul et al 1990 ). The alignments were then ordered based on linkage group ID and cM distance, using only the alignments with the highest percent identity and evalue scores to identify contig order.…”

“…The high demand for, and economic importance of, avocados motivates breeding efforts, but breeding remains challenging for at least 3 reasons. First, the avocado is a large tree that matures slowly [5–8 years before production ( Lahav and Lavi 2009 )] requiring substantial space, water, and finances ( Ashworth et al 2019 ). A second major obstacle is the reproductive system.…”

Insights into the domestication of avocado and potential genetic contributors to heterodichogamy

“…HapSolo v0.1 (Solares et al ., 2021), which identifies and removes alternative haplotypes, was then run on the assembly with default parameters and 50,000 iterations, producing the Canu+Hapsolo (C+H) assembly. Scaffolding was based on a Gwen x Fuerte genetic map (Ashworth et al ., 2019) by aligning the C+H assembly using NCBI BLAST v2.2.31+ (Altschul et al ., 1990). The alignments were then ordered based on linkage group ID and cM distance, using only the alignments with the highest percent identity and evalue scores to identify contig order.…”

“…The high demand for, and economic importance of, avocados motivates breeding efforts, but breeding remains challenging for at least three reasons. First, avocado is a large tree that matures slowly [5 to 8 years before production (Lahav & Lavi, 2009)] requiring substantial space, water and finances (Ashworth et al ., 2019). A second major obstacle is the reproductive system.…”