Interval mapping for red/green skin color in Asian pears using a modified QTL-seq method

Area of Science:

• Plant genetics
• Horticultural science
• Molecular breeding

Background:

• Red skin pears are desirable for consumers due to aesthetic appeal and health benefits.
• Identifying genes for red skin color is crucial for improving Asian pear cultivars through selective breeding.
• Existing QTL-seq methods face challenges with highly heterozygous parents in genetic mapping.

Purpose of the Study:

• To enhance the accuracy of mapping the red skin trait in heterozygous Asian pears.
• To identify specific genetic markers associated with red skin coloration.
• To provide insights into the genetic control of the red skin phenotype in pears.

Main Methods:

• Modified QTL-seq by introducing a |Δ(SNP-index)| parameter for improved mapping accuracy.
• Utilized mixed DNA pools from red and green-skinned Asian pear lines derived from a specific cross.
• Employed a sliding window approach for calculating average single-nucleotide polymorphism (SNP) index and identified candidate QTL intervals.

Main Results:

• Identified a 582.5-kb candidate interval on the fifth chromosome containing 81 predicted protein-coding genes associated with the red/green skin (R/G) locus.
• Established significant linkage between insertion/deletion and SSR markers and the R/G locus.
• Pinpointed specific markers (ZFRI 130-16, In2130-12, In2130-16) near the R/G locus for potential use in identifying red skin traits.

Conclusions:

• The modified QTL-seq method with |Δ(SNP-index)| effectively maps traits in heterozygous populations.
• The identified genetic region and markers provide valuable tools for marker-assisted selection in Asian pear breeding.
• This research advances the understanding of the genetic basis for red skin color in pears.