High-Resolution Linkage Map and QTL Analyses for Machine Harvest Traits in Autotetraploid Blueberry

Abstract

2Blueberry (Vacciunium corymbosum and hybrids) is an autotetraploid crop whose commercial 3 relevance has been growing steadily during the last twenty years. However, the ever-increasing 4 cost of labor for hand-picking blueberry is one main constraint in competitive marketing of the 5 fruit. Machine harvestability is, therefore, a key trait for the blueberry industry. Understanding 6 the genetic architecture of traits through quantitative trait locus (QTL) mapping is the first step 7 towards implementation of molecular breeding for faster genetic gains. Despite recent advances 8 in software development for autotetraploid genetic mapping, a high-resolution map is still not 9 available for blueberry. In this study, we crafted a map for autotetraploid low-chill highbush 10 blueberry containing 11,292 SNP markers and a total size of 1,953.97 cM (average density of 11 5.78 markers/cM). This map was subsequently used to perform QTL analyses for traits relevant 12 to machine harvesting: firmness, firmness retention, and fruit detachment force. Significant 13 QTL peaks were identified for all the traits. The QTL intervals were further explored for putative 14 candidate genes. Genes related to cell wall remodeling were highlighted in the firmness and 15 firmness retention intervals. For fruit detachment force, transcription factors involved in fruit 16 abscission were detected. Altogether, our findings provide the basis for future fine-mapping and 17 molecular breeding efforts for machine harvesting in blueberry. 18 Keywords: Vaccinium, southern highbush blueberry, firmness, detachment force, polyploid 19 20chromosomal alterations are not only tolerated by plant genomes, but can also drive evolution, for example, 21 promoting speciation (Adams and Wendel, 2005). Polyploid organisms are classified as either allopolyploids 22 or autopolyploids, depending on the degree of divergence between their subgenomes (Brubaker et al., 1999). 23 Autopolyploids, such as blueberry (Vaccinium corymbosum L.), potato (Solanum tuberosum L.), and alfalfa 24 (Medicago sativa L.), contain multiple copies of the same chromosome set, which can all pair and exchange 25 1 Cappai et al. QTL Map for Blueberry Harvest genetic material during gamete formation. In contrast, allopolyploids, such as wheat (Triticum aestivum 26 L.), coffee (Coffea arabica L.), and strawberry (Fragaria ananassa Duch.) contain two or more divergent 27 genomes, which usually show bivalent pairing and have disomic inheritance, like diploid organisms. 28 While in diploid systems the study of allelic inheritance is relatively simple, polysomic inheritance in 29 autopolyploids increases the number of possible genetic configurations and impacts downstream genetic 30 analyses, including linkage map construction and quantitative trait loci (QTL) mapping (Bever and Felber, 31 1992). 32 QTL mapping is the association study between phenotypic and genetic variants usually performed by 33 tracking recombination events of the possible QTL along chromosomes (Broman and Sen, 2009). In 34 b...

There and back again; historical perspective and future directions for Vaccinium breeding and research studies

“…sequencing of amplicon or baited target capture) approaches to high throughput genotyping are in use, whereas, in cranberry only GBS has been utilized thus far. GBS has been used in blueberry for the analysis of genetic diversity [ 142 , 143 ], linkage mapping [ 144 – 146 ], QTL analysis [ 144 , 145 ], and to validate F1 hybrids of V. padifolium x V. corymbosum [ 16 ]. Genome-wide SNP data identified via ddRAD-seq indicated admixture in southern highbush blueberry and suggested a polygenic adaptation to low chill conditions [ 147 ].…”