A high-recovery, high-density targeted genotyping platform for cranberry

Area of Science:

• Plant genetics
• Agricultural science
• Bioinformatics

Background:

• American cranberry (Vaccinium macrocarpon) is a significant commercial berry crop with recognized health benefits.
• Genotyping-by-sequencing (GBS) was the primary high-throughput genotyping method in cranberry, but it has limitations in data transferability.
• Existing GBS methods in cranberry lack the ability to easily transfer variant calls between populations and studies.

Purpose of the Study:

• To develop and characterize the first targeted high-throughput genotyping platform for American cranberry.
• To assess the performance of the new platform in terms of marker density, recovery rate, and accuracy.
• To evaluate the platform's utility in quantitative trait loci (QTL) analysis and assessing genetic relatedness.

Main Methods:

• Development of the Flex-Seq genotyping technology for cranberry, targeting 17,502 loci.
• Evaluation of the platform's recovery rate using a diversity panel of 192 cranberry accessions.
• Analysis of parent-offspring trios to determine the level of incompatible marker inheritance and assess parentage accuracy.
• Comparison of Flex-Seq performance against GBS in QTL analyses and relatedness studies.

Main Results:

• The Flex-Seq platform achieved a high recovery rate of 99.8% across 192 cranberry accessions.
• Incompatible marker inheritance averaged 5.5% across 22 parent-offspring trios, with some indicating potential inconsistencies for further investigation.
• Flex-Seq identified more QTLs and higher logarithm of odds scores than GBS, and locus haplotypes improved relatedness resolution.

Conclusions:

• The developed Flex-Seq platform is a repeatable, high-recovery, high-density genotyping tool for cranberry.
• This technology offers significant advantages over GBS for trait mapping precision and genetic relatedness analysis.
• The platform will accelerate the improvement of cranberry cultivars by enabling better utilization of genetic resources and robust accession characterization.