Breeding and genetics of disease resistance in temperate fruit trees: challenges and new opportunities

Khan, Awais; Korban, Schuyler S.

doi:10.1007/s00122-022-04093-0

Cited by 35 publications

(25 citation statements)

References 183 publications

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“…Indeed, in the last decade since 'Golden Delicious' was sequenced [27], many genes and quantitative trait loci (QTL) linked to fruit disease resistance, quality traits, and abiotic stress tolerance in apples have been identified [7,28,29]. Recent high-quality genomes of 'Gala', the double haploid 'Golden Delicious', and the triploid 'Hanfu' provide genomic resources for apple genetics and breeding [27,30,31].…”

Section: Contextmentioning

confidence: 99%

A phased, chromosome-scale genome of ‘Honeycrisp’ apple (Malus domestica)

et al. 2022

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The apple cultivar ‘Honeycrisp’ has superior fruit quality traits, cold hardiness, and disease resistance, making it a popular breeding parent. However, it suffers from several physiological disorders, production, and postharvest issues. Despite several available apple genome sequences, understanding of the genetic mechanisms underlying cultivar-specific traits remains lacking. Here, we present a highly contiguous, fully phased, chromosome-level genome of ‘Honeycrisp’ apples, using PacBio HiFi, Omni-C, and Illumina sequencing platforms, with two assembled haplomes of 674 Mbp and 660 Mbp, and contig N50 values of 32.8 Mbp and 31.6 Mbp, respectively. Overall, 47,563 and 48,655 protein-coding genes were annotated from each haplome, capturing 96.8–97.4% complete BUSCOs in the eudicot database. Gene family analysis reveals most ‘Honeycrisp’ genes are assigned into orthogroups shared with other genomes, with 121 ‘Honeycrisp’-specific orthogroups. This resource is valuable for understanding the genetic basis of important traits in apples and related Rosaceae species to enhance breeding efforts.

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Section: Contextmentioning

confidence: 99%

A phased, chromosome-scale genome of ‘Honeycrisp’ apple (Malus domestica)

et al. 2022

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“…Current cultivation of perennial crops such as fruit trees and grapevine relies heavily on chemical pest and disease control, and both breeding and adoption of new cultivars are typically slow. New ways and new tools to accelerate cultivar resistance for grapevine (Topfer and Trapp 2022) and perennial fruit trees (Khan and Korban 2022) are therefore urgently needed.…”

Section: Challenges Opportunities and Progressmentioning

confidence: 99%

Plant breeding for increased sustainability: challenges, opportunities and progress

et al. 2022

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Humanity is facing enormous challenges in the years to come: sustainability of agriculture and sustainability of our supply with food, feed and renewable materials are neither granted nor free. Especially, but not only, in the Global South, a sustainable increase in agricultural productivity and a steady reduction of avoidable losses are undoubtedly key issues that need to be addressed.In order to pinpoint the most pressing challenges and strategies to achieve targets, the United Nations have formulated the Sustainable Development Goals (https:// sdgs. un. org/ goals). Among these, several are directly or indirectly addressing agriculture, food supply and sustainability, most notably SDG2 (zero hunger), SDG12 (responsible consumption and production), SDG13 (climate action) and SDG15 (life on land).

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“…These studies have identified targeted genomic regions for the development of diagnostic molecular markers to breed disease resistant apple cultivars with good fruit quality [30]. However, the fact remains that traditional apple breeding is a resource-intensive and time-consuming process [9,26,30] and there are still substantial gaps in our knowledge of genetic mechanisms involved in many important apple traits. In this manuscript we report a phased, chromosome-level genome assembly of the ‘Honeycrisp’ apple cultivar generated from PacBio HiFi and Dovetail Omni-C, plus a high-quality annotation – thus providing one of the best genome resources available for apples to date.…”

Section: Introductionmentioning

confidence: 99%

“…To maximize both our understanding of genetic mechanisms driving important 'Honeycrisp' traits and to assist tree fruit breeders, high quality genomes are required [23]. Indeed, in the last decade since 'Golden Delicious' was sequenced [24], a large number of genes and QTLs linked to fruit disease resistance, quality traits, and abiotic stress tolerance in apples have been identified [5,25,26]. Recent high-quality genomes of 'Gala', the double haploid 'Golden Delicious', and the triploid 'Hanfu' provide genomic resources for apple genetics and breeding [27][28][29].…”

Section: Introductionmentioning

confidence: 99%

A phased, chromosome-scale genome of ‘Honeycrisp’ apple (Malus domestica)

Khan

Carey

Serrano

et al. 2022

Preprint

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′Honeycrisp′ is one of the most valuable apple cultivars grown in the United States and a popular breeding parent due to its superior fruit quality traits, high levels of cold hardiness, and disease resistance. However, it suffers from a number of physiological disorders and is susceptible to production and postharvest issues. Although several apple genomes have been sequenced in the last decade, there is still a substantial knowledge gap in understanding the genetic mechanisms underlying cultivar-specific traits. Here we present a fully phased, chromosome-level genome of the ′Honeycrisp′ apples, using PacBio HiFi, Omni-C, and Illumina sequencing platforms. Our genome assembly is by far the most contiguous among all the apple genomes. The sizes of the two assembled haplomes are 674 Mb and 660 Mb, with contig N50s of 32.8 Mb and 31.6 Mb, respectively. In total, 47,563 and 48,655 protein coding genes were annotated from each haplome, capturing 96.8-97.4% complete BUSCOs in the eudicot database, the most complete among all Malus annotations. A gene family analysis using seven Malus genomes shows that a vast majority of ′Honeycrisp′ genes are assigned into orthogroups shared with other genomes, but it also reveals 121 ′Honeycrisp′-specific orthogroups. We provide a valuable resource for understanding the genetic basis of horticulturally important traits in apples and other related tree fruit species, including at-harvest and postharvest fruit quality, abiotic stress tolerance, and disease resistance, all of which can enhance breeding efforts in Rosaceae.

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Breeding and genetics of disease resistance in temperate fruit trees: challenges and new opportunities

Cited by 35 publications

References 183 publications

A phased, chromosome-scale genome of ‘Honeycrisp’ apple (Malus domestica)

A phased, chromosome-scale genome of ‘Honeycrisp’ apple (Malus domestica)

Plant breeding for increased sustainability: challenges, opportunities and progress

A phased, chromosome-scale genome of ‘Honeycrisp’ apple (Malus domestica)

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