Apples are a nutritious food source with significant amounts of polyphenols that contribute to human health and wellbeing,primarily as dietary antioxidants.Although numerous pre-and post-harvest factors can affect the...Apples are a nutritious food source with significant amounts of polyphenols that contribute to human health and wellbeing,primarily as dietary antioxidants.Although numerous pre-and post-harvest factors can affect the composition of polyphenols in apples,genetics is presumed to play a major role because polyphenol concentration varies dramatically among apple cultivars.Here we investigated the genetic architecture of apple polyphenols by combining high performance liquid chromatography(HPLC)data with~100,000 single nucleotide polymorphisms(SNPs)from two diverse apple populations.We found that polyphenols can vary in concentration by up to two orders of magnitude across cultivars,and that this dramatic variation was often predictable using genetic markers and frequently controlled by a small number of large effect genetic loci.Using GWAS,we identified candidate genes for the production of quercitrin,epicatechin,catechin,chlorogenic acid,4-O-caffeoylquinic acid and procyanidins B1,B2,and C1.Our observation that a relatively simple genetic architecture underlies the dramatic variation of key polyphenols in apples suggests that breeders may be able to improve the nutritional value of apples through markerassisted breeding or gene editing.展开更多
Grapes are one of the most economically and culturally important crops worldwide,and they have been bred for both winemaking and fresh consumption.Here we evaluate patterns of diversity across 33 phenotypes collected ...Grapes are one of the most economically and culturally important crops worldwide,and they have been bred for both winemaking and fresh consumption.Here we evaluate patterns of diversity across 33 phenotypes collected over a 17-year period from 580 table and wine grape accessions that belong to one of the world’s largest grape gene banks,the grape germplasm collection of the United States Department of Agriculture.We find that phenological events throughout the growing season are correlated,and quantify the marked difference in size between table and wine grapes.By pairing publicly available historical phenotype data with genome-wide polymorphism data,we identify large effect loci controlling traits that have been targeted during domestication and breeding,including hermaphroditism,lighter skin pigmentation and muscat aroma.Breeding for larger berries in table grapes was traditionally concentrated in geographic regions where Islam predominates and alcohol was prohibited,whereas wine grapes retained the ancestral smaller size that is more desirable for winemaking in predominantly Christian regions.We uncover a novel locus with a suggestive association with berry size that harbors a signature of positive selection for larger berries.Our results suggest that religious rules concerning alcohol consumption have had a marked impact on patterns of phenomic and genomic diversity in grapes.展开更多
In 2010,a major scientific milestone was achieved for tree fruit crops:publication of the first draft whole genome sequence(WGS)for apple(Malus domestica).This WGS,v1.0,was valuable as the initial reference for sequen...In 2010,a major scientific milestone was achieved for tree fruit crops:publication of the first draft whole genome sequence(WGS)for apple(Malus domestica).This WGS,v1.0,was valuable as the initial reference for sequence information,fine mapping,gene discovery,variant discovery,and tool development.A new,high quality apple WGS,GDDH13 v1.1,was released in 2017 and now serves as the reference genome for apple.Over the past decade,these apple WGSs have had an enormous impact on our understanding of apple biological functioning,trait physiology and inheritance,leading to practical applications for improving this highly valued crop.Causal gene identities for phenotypes of fundamental and practical interest can today be discovered much more rapidly.Genome-wide polymorphisms at high genetic resolution are screened efficiently over hundreds to thousands of individuals with new insights into genetic relationships and pedigrees.High-density genetic maps are constructed efficiently and quantitative trait loci for valuable traits are readily associated with positional candidate genes and/or converted into diagnostic tests for breeders.We understand the species,geographical,and genomic origins of domesticated apple more precisely,as well as its relationship to wild relatives.The WGS has turbo-charged application of these classical research steps to crop improvement and drives innovative methods to achieve more durable,environmentally sound,productive,and consumer-desirable apple production.This review includes examples of basic and practical breakthroughs and challenges in using the apple WGSs.Recommendations for“what’s next”focus on necessary upgrades to the genome sequence data pool,as well as for use of the data,to reach new frontiers in genomics-based scientific understanding of apple.展开更多
The apple(Malus domestica)is one of the world's most commercially important perennial crops and its improvement has been the focus of human effort for thousands of years.Here,we genetically characterise over 1000 ...The apple(Malus domestica)is one of the world's most commercially important perennial crops and its improvement has been the focus of human effort for thousands of years.Here,we genetically characterise over 1000 apple accessions from the United States Department of Agriculture(USDA)germplasm collection using over 30,000 singlenucleotide polymorphisms(SNPs).We con fi rm the close genetic relationship between modern apple cultivars and their primary progenitor species,Malus sieversii from Central Asia,and fi nd that cider apples derive more of their ancestry from the European crabapple,Malus sylvestris,than do dessert apples.We determine that most of the USDA collection is a large complex pedigree:over half of the collection is interconnected by a series of fi rst-degree relationships.In addition,15%of the accessions have a fi rst-degree relationship with one of the top 8 cultivars produced in the USA.With the exception of‘Honeycrisp',the top 8 cultivars are interconnected to each other via pedigree relationships.The cultivars‘Golden Delicious'and‘Red Delicious'were found to have over 60 fi rst-degree relatives,consistent with their repeated use by apple breeders.We detected a signature of intense selection for red skin and provide evidence that breeders also selected for increased fi rmness.Our results suggest that Americans are eating apples largely from a single family tree and that the apple's future improvement will bene fi t from increased exploitation of its tremendous natural genetic diversity.展开更多
The apple(Malus×domestica Borkh.)is one of the world’s most widely grown and valuable fruit crops.With demand for apples year round,storability has emerged as an important consideration for apple breeding progra...The apple(Malus×domestica Borkh.)is one of the world’s most widely grown and valuable fruit crops.With demand for apples year round,storability has emerged as an important consideration for apple breeding programs.Soft scald is a cold storage-related disorder that results in sunken,darkened tissue on the fruit surface.Apple breeders are keen to generate new cultivars that do not suffer from soft scald and can thus be marketed year round.Traditional breeding approaches are protracted and labor intensive,and therefore marker-assisted selection(MAS)is a valuable tool for breeders.To advance MAS for storage disorders in apple,we used genotyping-by-sequencing(GBS)to generate high-density genetic maps in two F1 apple populations,which were then used for quantitative trait locus(QTL)mapping of soft scald.In total,900 million DNA sequence reads were generated,but after several data filtering steps,only 2%of reads were ultimately used to create two genetic maps that included 1918 and 2818 single-nucleotide polymorphisms.Two QTL associated with soft scald were identified in one of the bi-parental populations originating from parent 11W-12-11,an advanced breeding line.This study demonstrates the utility of next-generation DNA sequencing technologies for QTL mapping in F1 populations,and provides a basis for the advancement of MAS to improve storability of apples.展开更多
基金supported in part by funding from the Canada Research Chairs program(SM),the National Sciences and Engineering Research Council of Canada(SM),and A-Base funding(NOI-1767)from Agriculture and Agri-Food Canada(JS).ZM was supported by NSF 1546869.
文摘Apples are a nutritious food source with significant amounts of polyphenols that contribute to human health and wellbeing,primarily as dietary antioxidants.Although numerous pre-and post-harvest factors can affect the composition of polyphenols in apples,genetics is presumed to play a major role because polyphenol concentration varies dramatically among apple cultivars.Here we investigated the genetic architecture of apple polyphenols by combining high performance liquid chromatography(HPLC)data with~100,000 single nucleotide polymorphisms(SNPs)from two diverse apple populations.We found that polyphenols can vary in concentration by up to two orders of magnitude across cultivars,and that this dramatic variation was often predictable using genetic markers and frequently controlled by a small number of large effect genetic loci.Using GWAS,we identified candidate genes for the production of quercitrin,epicatechin,catechin,chlorogenic acid,4-O-caffeoylquinic acid and procyanidins B1,B2,and C1.Our observation that a relatively simple genetic architecture underlies the dramatic variation of key polyphenols in apples suggests that breeders may be able to improve the nutritional value of apples through markerassisted breeding or gene editing.
基金We acknowledge the funding from the Canada Research Chairs program,the National Sciences and Engineering Research Council of Canada and Genome CanadaZM was supported in part by a Killam Predoctoral Scholarship from Dalhousie University.
文摘Grapes are one of the most economically and culturally important crops worldwide,and they have been bred for both winemaking and fresh consumption.Here we evaluate patterns of diversity across 33 phenotypes collected over a 17-year period from 580 table and wine grape accessions that belong to one of the world’s largest grape gene banks,the grape germplasm collection of the United States Department of Agriculture.We find that phenological events throughout the growing season are correlated,and quantify the marked difference in size between table and wine grapes.By pairing publicly available historical phenotype data with genome-wide polymorphism data,we identify large effect loci controlling traits that have been targeted during domestication and breeding,including hermaphroditism,lighter skin pigmentation and muscat aroma.Breeding for larger berries in table grapes was traditionally concentrated in geographic regions where Islam predominates and alcohol was prohibited,whereas wine grapes retained the ancestral smaller size that is more desirable for winemaking in predominantly Christian regions.We uncover a novel locus with a suggestive association with berry size that harbors a signature of positive selection for larger berries.Our results suggest that religious rules concerning alcohol consumption have had a marked impact on patterns of phenomic and genomic diversity in grapes.
文摘In 2010,a major scientific milestone was achieved for tree fruit crops:publication of the first draft whole genome sequence(WGS)for apple(Malus domestica).This WGS,v1.0,was valuable as the initial reference for sequence information,fine mapping,gene discovery,variant discovery,and tool development.A new,high quality apple WGS,GDDH13 v1.1,was released in 2017 and now serves as the reference genome for apple.Over the past decade,these apple WGSs have had an enormous impact on our understanding of apple biological functioning,trait physiology and inheritance,leading to practical applications for improving this highly valued crop.Causal gene identities for phenotypes of fundamental and practical interest can today be discovered much more rapidly.Genome-wide polymorphisms at high genetic resolution are screened efficiently over hundreds to thousands of individuals with new insights into genetic relationships and pedigrees.High-density genetic maps are constructed efficiently and quantitative trait loci for valuable traits are readily associated with positional candidate genes and/or converted into diagnostic tests for breeders.We understand the species,geographical,and genomic origins of domesticated apple more precisely,as well as its relationship to wild relatives.The WGS has turbo-charged application of these classical research steps to crop improvement and drives innovative methods to achieve more durable,environmentally sound,productive,and consumer-desirable apple production.This review includes examples of basic and practical breakthroughs and challenges in using the apple WGSs.Recommendations for“what’s next”focus on necessary upgrades to the genome sequence data pool,as well as for use of the data,to reach new frontiers in genomics-based scientific understanding of apple.
基金funding from the National Sciences and Engineering Research Council of Canada and Canada Research Chairs programme(SM).
文摘The apple(Malus domestica)is one of the world's most commercially important perennial crops and its improvement has been the focus of human effort for thousands of years.Here,we genetically characterise over 1000 apple accessions from the United States Department of Agriculture(USDA)germplasm collection using over 30,000 singlenucleotide polymorphisms(SNPs).We con fi rm the close genetic relationship between modern apple cultivars and their primary progenitor species,Malus sieversii from Central Asia,and fi nd that cider apples derive more of their ancestry from the European crabapple,Malus sylvestris,than do dessert apples.We determine that most of the USDA collection is a large complex pedigree:over half of the collection is interconnected by a series of fi rst-degree relationships.In addition,15%of the accessions have a fi rst-degree relationship with one of the top 8 cultivars produced in the USA.With the exception of‘Honeycrisp',the top 8 cultivars are interconnected to each other via pedigree relationships.The cultivars‘Golden Delicious'and‘Red Delicious'were found to have over 60 fi rst-degree relatives,consistent with their repeated use by apple breeders.We detected a signature of intense selection for red skin and provide evidence that breeders also selected for increased fi rmness.Our results suggest that Americans are eating apples largely from a single family tree and that the apple's future improvement will bene fi t from increased exploitation of its tremendous natural genetic diversity.
基金This project was funded by the A-Base research(NOI-1238)of Agriculture and Agri-Food CanadaThis research was also supported in part by funding from the Canada Research Chairs program(SM)and the National Sciences and Engineering Research Council of Canada(SM,KM).
文摘The apple(Malus×domestica Borkh.)is one of the world’s most widely grown and valuable fruit crops.With demand for apples year round,storability has emerged as an important consideration for apple breeding programs.Soft scald is a cold storage-related disorder that results in sunken,darkened tissue on the fruit surface.Apple breeders are keen to generate new cultivars that do not suffer from soft scald and can thus be marketed year round.Traditional breeding approaches are protracted and labor intensive,and therefore marker-assisted selection(MAS)is a valuable tool for breeders.To advance MAS for storage disorders in apple,we used genotyping-by-sequencing(GBS)to generate high-density genetic maps in two F1 apple populations,which were then used for quantitative trait locus(QTL)mapping of soft scald.In total,900 million DNA sequence reads were generated,but after several data filtering steps,only 2%of reads were ultimately used to create two genetic maps that included 1918 and 2818 single-nucleotide polymorphisms.Two QTL associated with soft scald were identified in one of the bi-parental populations originating from parent 11W-12-11,an advanced breeding line.This study demonstrates the utility of next-generation DNA sequencing technologies for QTL mapping in F1 populations,and provides a basis for the advancement of MAS to improve storability of apples.
