Genetic and genomic resources for Rubus breeding:a roadmap for the future

Rubus fruits are high-value crops that are sought after by consumers for their flavor,visual appeal,and health benefits.To meet this demand,production of red and black raspberries(R.idaeus L.and R.occidentalis L.),blackberries(R.subgenus Rubus),and hybrids,such as Boysenberry and marionberry,is growing worldwide.Rubus breeding programmes are continually striving to improve flavor,texture,machine harvestability,and yield,provide pest and disease resistance,improve storage and processing properties,and optimize fruits and plants for different production and harvest systems.Breeders face numerous challenges,such as polyploidy,the lack of genetic diversity in many of the elite cultivars,and until recently,the relative shortage of genetic and genomic resources available for Rubus.This review will highlight the development of continually improving genetic maps,the identification of Quantitative Trait Loci(QTL)s controlling key traits,draft genomes for red and black raspberry,and efforts to improve gene models.The development of genetic maps and markers,the molecular characterization of wild species and germplasm,and highthroughput genotyping platforms will expedite breeding of improved cultivars.Fully sequenced genomes and accurate gene models facilitate identification of genes underlying traits of interest and enable gene editing technologies such as CRISPR/Cas9.

Seeing the wood for the trees:hyperspectral imaging for high throughput QTL detection in raspberry,a perennial crop species

Physiological and physical traits are excellent indicators of many crop characteristics,but precise phenotyping of these traits is time consuming and,therefore,limits progress in crop breeding and the speed of crop monitoring.Hyperspectral imaging offers an opportunity to overcome these barriers as a technique for high throughput field measurements.Using a recently developed hyperspectral imaging platform devised for plantations of the perennial crop raspberry,this study aimed to further develop the tool and test its capacity as an innovative approach for high throughput field phenotyping,data collection and analysis.Hyperspectral imaging and visual crop assessments were carried out over two growing seasons in a field-grown raspberry mapping population,and data were subject to Quantitative Trait Loci(QTL)analysis.The findings show that reflectance intensity at multiple wavelengths can be linked to known genetic markers in raspberry,and many of these‘spectral traits'are expressed consistently through the growing season and between years,for example spectral ratio 719 nm/691 nm shows up consistently as a QTL on LG4.Spectral traits were identified that co-located with previously mapped physical traits,such as 719 nm/691 nm and cane density.The study indicates that hyperspectral imaging can be used as an innovative approach for high throughput field phenotyping of raspberry and could be transferred readily to other perennial crops.Our approach provides a pipeline for automated field data collection and analysis that can be used for rapid QTL detection of spectral traits.