Genome-Assisted Breeding in the Octoploid Strawberry

Verma, Sujeet; Osorio, Luis F.; Lee, Seong-Hee; Bassil, Nahla V.; Whitaker, Vance M.

doi:10.1007/978-3-319-76020-9_12

Cited by 8 publications

(12 citation statements)

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“…An analysis of diploid R-genes across the Rosaceae genus was previously conducted (Arya et al 2014). New genetic resources for high-resolution genotyping in octoploid strawberry have resulted in the recent identification of several disease resistance loci (Mangandi et al 2017; Nellist et al 2019; Cockerton et al 2018; Pincot et al 2018; Salinas et al 2018; Anciro et al 2018; Roach et al 2016; Verma et al 2018). However, the specific genes mediating resistance in these QTL intervals typically remain unresolved, as genomic resources for octoploid strawberry have not kept pace with genetic mapping.…”

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Disease Resistance Genetics and Genomics in Octoploid Strawberry

Barbey

Lee

Verma

et al. 2019

G3 Genes|Genomes|Genetics

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Octoploid strawberry (Fragaria ×ananassa) is a valuable specialty crop, but profitable production and availability are threatened by many pathogens. Efforts to identify and introgress useful disease resistance genes (R-genes) in breeding programs are complicated by strawberry’s complex octoploid genome. Recently-developed resources in strawberry, including a complete octoploid reference genome and high-resolution octoploid genotyping, enable new analyses in strawberry disease resistance genetics. This study characterizes the complete R-gene collection in the genomes of commercial octoploid strawberry and two diploid ancestral relatives, and introduces several new technological and data resources for strawberry disease resistance research. These include octoploid R-gene transcription profiling, dN/dS analysis, expression quantitative trait loci (eQTL) analysis and RenSeq analysis in cultivars. Octoploid fruit eQTL were identified for 76 putative R-genes. R-genes from the ancestral diploids Fragaria vesca and Fragaria iinumae were compared, revealing differential inheritance and retention of various octoploid R-gene subtypes. The mode and magnitude of natural selection of individual F. ×ananassa R-genes was also determined via dN/dS analysis. R-gene sequencing using enriched libraries (RenSeq) has been used recently for R-gene discovery in many crops, however this technique somewhat relies upon a priori knowledge of desired sequences. An octoploid strawberry capture-probe panel, derived from the results of this study, is validated in a RenSeq experiment and is presented for community use. These results give unprecedented insight into crop disease resistance genetics, and represent an advance toward exploiting variation for strawberry cultivar improvement.

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Disease Resistance Genetics and Genomics in Octoploid Strawberry

Barbey

Lee

Verma

et al. 2019

G3 Genes|Genomes|Genetics

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“…glauca [60]. Verma et al [61] reported that this QTL was intensely utilized in the strawberry breeding program at UC Davis [62]. The determined QTL had a single dominant allele on one sub-genome governing the transformation from short-day to day-neutrality [59].…”

Section: Qtls Related To the Morphological And Biochemical Traits In ...mentioning

confidence: 99%

“…The locus ChFaM148-184 T was found highly linked with this QTL and the total phenotypic explained variation was 32.4%. Verma et al [61] stated that they performed the QTL analysis related to the day-neutrality in the RosBREED strawberry germplasm dataset. The results demonstrated that there is a major QTL in the same linkage group, LG IV [61].…”

Section: Qtls Related To the Morphological And Biochemical Traits In ...mentioning

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Quantitative Trait Loci Associated with Agronomical Traits in Strawberry

Karcı¹,

Tevfik²,

Kafkas³

et al. 2023

Recent Studies on Strawberries

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The cultivated strawberry (Fragaria x ananassa) is derived from Fragaria chiloensis and Fragaria virginiana species a few centuries ago, and it is one of the most preferred and consumed berries all over the world because of its a good source in terms of many nutritional elements. Strawberry has high genetic variability and adaptation to different environmental conditions due to its highly heterozygous nature. In the last decades, many farmers, breeders, researchers even consumers have started to focus on berry quality traits such as large fruit, uniform shape, high fruit firmness, high fruit sensorial quality (aroma contents), color, gloss, and resistance to pathogens. Thus, the development of novel strawberry cultivars or genotypes with high nutritionally quality traits has become one of the main aims in strawberry breeding programs. Biotechnological tools such as the identification of quantitative trait loci (QTL) and marker-assisted selection (MAS) are the most widely used technologies in fruit breeding programs for shortening the breeding period. Identification of QTLs in agnomical important traits are very valuable tools for early selection in strawberry breeding programs. This chapter is focused on QTL and marker assisted breeding studies in strawberry to date and provides new perspectives on molecular breeding in strawberry breeding.

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“…Genetic disease resistance 52 has been a long-standing breeding priority. While breeders have made progress in producing 53 varieties with tolerance to some pathogens, growers remain dependent on exogenous crop Verma et al, 2018). However, the specific 73 genes mediating resistance in these QTL intervals typically remain unresolved, as genomic 74 resources for octoploid strawberry have not kept pace with genetic mapping.…”

Section: Introductionmentioning

confidence: 99%

Disease Resistance Genetics and Genomics in Octoploid Strawberry

Barbey

Lee

Verma

et al. 2019

Preprint

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25Octoploid strawberry (Fragaria ×ananassa) is a valuable specialty crop, but profitable production 26 and availability are threatened by many pathogens. Efforts to identify and introgress useful disease 27 resistance genes (R-genes) in breeding programs are complicated by strawberry's complex 28 octoploid genome. Recently-developed resources in strawberry, including a complete octoploid 29 reference genome and high-resolution octoploid genotyping, enable new analyses in strawberry 30 disease resistance genetics. This study characterizes the complete R-gene collection in the 31 genomes of commercial octoploid strawberry and two diploid ancestral relatives, and introduces 32 several new technological and data resources for strawberry disease resistance research. These 33 include octoploid R-gene transcription profiling, dN/dS analysis, eQTL analysis and RenSeq 34 analysis in cultivars. Octoploid fruit transcript expression quantitative trait loci (eQTL) were 35 identified for 77 putative R-genes. R-genes from the ancestral diploids Fragaria vesca and 36 Fragaria iinumae were compared, revealing differential inheritance and retention of various 37 octoploid R-gene subtypes. The mode and magnitude of natural selection of individual F. 38 ×ananassa R-genes was also determined via dN/dS analysis. R-gene sequencing using enriched 39 libraries (RenSeq) has been used recently for R-gene discovery in many crops, however this 40 technique somewhat relies upon a priori knowledge of desired sequences. An octoploid strawberry 41 capture-probe panel, derived from the results of this study, is validated in a RenSeq experiment 42 and is presented for community use. These results give unprecedented insight into crop disease 43 resistance genetics, and represent an advance towards exploiting variation for strawberry cultivar 44 improvement. 45 46 102 for fully exploiting genetic disease resistance in strawberry. This research introduces several new 103 technology and data resources that now may be applied in study of strawberry disease resistance. 104 105 106 6 RESULTS 107 Octoploid and Diploid R-genes 108

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Genome-Assisted Breeding in the Octoploid Strawberry

Cited by 8 publications

References 103 publications

Disease Resistance Genetics and Genomics in Octoploid Strawberry

Disease Resistance Genetics and Genomics in Octoploid Strawberry

Quantitative Trait Loci Associated with Agronomical Traits in Strawberry

Disease Resistance Genetics and Genomics in Octoploid Strawberry

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