Hackett, C.A., Milne, L., Smith, K., Hedley, P.E., Morris, J.A., Simpson, C.G., Preedy, K. and Graham, J.
raspberry, GbS, linkage analysis, QTL mapping, hidden Markov model, fruit development, ripening
||Background: The changing climate is altering the timing of key processed around fruit ripening and also increasing the occurrence of fruit defects. Therefore, to improve our understanding of the genetic control of commercial raspberry fruit development this work set out to develop an enhanced genetic linkage map and use this to examine ripening data.
Results: In this article we developed an enhanced genetic linkage map for the raspberry cvs. Glen Moy x Latham reference mapping population using genotyping by sequencing. By alignment to a newly sequenced draft reference genome of red raspberry, cv. Glen Moy, 8019 SNPs were identified and after stringent filtering to take account of read coverage over all the progeny individuals, association with a single chromosome, heterozygosity and marker regression mapping, 2348 high confidence SNPs were identified and mapped. The linkage map contained many more SNPs segregating in Latham than in Glen Moy. This caused difficulties in QTL mapping with standard software and a hidden Markov model was used to improve the mapping. Using previously described fruit ripening scores on this mapping population at two sites grown in open field and in polytunnel, QTL analysis generally confirmed the genetic locations found previously and identified some new regions.
Conclusion: The high-density GbS map located the QTL peaks more precisely, aligned the QTLs with Glen Moy genome scaffolds, narrowed the range of potential candidate genes to these regions and increased the numbers of precise markers available to understand the genetic control of fruit ripening specific traits.