Nature Genetics, Journal Year: 2025, Volume and Issue: unknown
Published: Feb. 26, 2025
Language: Английский
Trends in Plant Science, Journal Year: 2021, Volume and Issue: 26(6), P. 631 - 649
Published: April 21, 2021
Availability of reference genomes and genome-wide surveys on comprehensive diversity panels pave the way to associate allelic variation with phenotypes.Methods are now available evaluate genetic worth vast resources archived in gene banks streamline application these crop improvement programs.Precise genome editing technologies concert enhanced trait architectures enable innovative solutions engineer complex variation.High-throughput phenotyping methods beginning alleviate challenge accurate, precise, large-scale measurements plant performance.Optimized speed breeding protocols remain crucial accelerating advance when applied genomic approaches.Sustaining gains from seeks fast-tracking exploitation minor effect alleles, accumulation favorable purging deleterious alleles. Over past decade, genomics-assisted (GAB) has been instrumental harnessing potential modern characterizing exploiting for germplasm enhancement cultivar development. Sustaining GAB future (GAB 2.0) will rely upon a suite new approaches that fast-track targeted manipulation creating novel facilitate their rapid efficient incorporation programs. Genomic strategies optimize beneficial alleles be indispensable designing crops. In coming decades, 2.0 is expected play role more climate-smart cultivars higher nutritional value cost-effective timely manner. Ensuring sustainable increase global food production finite an increasing human population great challenge. wake enormous advances, 15 years back we proposed concept [1.Varshney R.K. et al.Genomics-assisted improvement.Trends Plant Sci. 2005; 10: 621-630Abstract Full Text PDF PubMed Scopus (392) Google Scholar]. Interestingly, proposition coincided release high-quality sequence assembly rice (Oryza sativa), representing first any [2.International Rice Genome Sequencing Project The map-based genome.Nature. 436: 793-800Crossref (2692) Subsequently, array tools have become applications (Table 1). Parallel advancements technologies, designs based multi-parent synthetic populations were implemented discovery impart benefits both association mapping linkage analysis, such as diversity, controlled structure, greater power quantitative locus (QTL) detection improved accuracy [3.Kover P.X. al.A multiparent advanced generation inter-cross fine-map traits Arabidopsis thaliana.PLoS Genet. 2009; 5e1000551Crossref (361) Scholar,4.Yu J. al.Genetic design statistical nested maize.Genetics. 2008; 178: 539-551Crossref (627) Scholar].Table 1Genome Resources Ten Topmost Food CropsaAbbreviation: n.d., no data.CropArea (mha)bSource: http://www.fao.org/faostat/en/#data/QC.Production (mmt)bSource: http://www.fao.org/faostat/en/#data/QC.Assembled (Mb)SNP arrayGenomic databasesGene expression atlasPan-genomeWheat(Triticum aestivum)215.9765.714 500[61.International Wheat Consortium (IWGSC) Shifting limits wheat research using fully annotated genome.Science. 2018; 361eaar7191Crossref (891) Scholar]Wheat 9K iSelect [62.Cavanagh C.R. al.Genome-wide comparative uncovers multiple targets selection hexaploid landraces cultivars.Proc. Natl. Acad. U. S. A. 2013; 110: 20Crossref (601) 90K [63.Wang Y. al.Simultaneous three homoeoalleles bread confers heritable resistance powdery mildew.Nat. Biotechnol. 2014; 32: 947-951Crossref (839) 660K Axiom HD genotyping [64.Winfield M.O. al.High-density SNP its secondary tertiary pool.Plant 2016; 14: 1195-1206Crossref (44) breeder's (Affymetrix 35K) [65.Allen A.M. al.Characterization breeders' suitable high-throughput accessions (Triticum aestivum).Plant 2017; 15: 390-401Crossref (0) Variation Database (WGVD) [66.Wang al.WGVD: integrated web-database selective signatures.Database. 2020; 2020baaa090Crossref Scholar]WheatExp [67.Pearce al.WheatExp: RNA-seq database polyploid wheat.BMC Biol. 2015; 299Crossref (59) Scholar]18 Cultivars [68.Montenegro J.D. al.The pangenome wheat.Plant 90: 1007-1013Crossref (111) Scholar]Maize(Zea mays)197.21148.42048[69.Schnable P.S. B73 maize genome: complexity, dynamics.Science. 326: 1112-1115Crossref (2568) Scholar]MaizeSNP50 BeadChip (llumina Infinium 50K) [70.Ganal M.W. large (Zea mays L.) array: development genotyping, compare genome.PLoS One. 2011; 6e28334Crossref Scholar]Subset MaizeSNP50 (Illumina 3K) [71.Rousselle al.Study essential derivation maize: III. Selection evaluation panel single nucleotide polymorphism loci use European North American germplasm.Crop 55: 1170-1180Crossref (3) Scholar]Axiom 600K [72.Unterseer powerful tool analysis high density 600 K array.BMC Genomics. 823Crossref 55K [73.Xu C. al.Development 55 coverage molecular breeding.Mol. Breed. 37: Scholar]MaizeSNPDB [74.Zhou W. al.MaizeSNPDB: retrieve SNPs among 1210 lines.Comput. Struct. 2019; 17: 1377-1383Crossref Scholar]36 207 Genes [75.Hoopes G.M. al.An updated atlas reveals organ-specific stress-induced genes.Plant 97: 1154-1167Crossref (29) Scholar]503 Inbred lines [76.Hirsch C.N. al.Insights into pan-genome pan-transcriptome.Plant Cell. 26: 121-135Crossref (226) Scholar]Rice(Oryza sativa)162755.4371[2.International Scholar]Affymetrix (1M) [77.McCouch S.R. assays rice.Breed. 2010; 60: 524-535Crossref (130) Scholar]RiceSNP50 [78.Chen analyses provide biochemical insights natural metabolism.Nat. 46: 714-721Crossref (293) Scholar]RICE6K 6K) [79.Yu H. whole-genome (RICE6K) rice.Plant 12: 28-37Crossref (101) Scholar] OsSNPnks [80.Singh N. al.Single-copy 50 chip studies rice.Sci. Rep. 5: 11600Crossref (34) Affymetrix GeneChip (44K) [81.Tung platform dissecting phenotype genotype associations spp.).Rice. 3: 205-217Crossref Scholar]SNP-Seek [82.Alexandrov al.SNP-Seek derived 3000 genomes.Nucleic Acids Res. 43: D1023-D1027Crossref (188) Scholar][83.Wang L. dynamic covering entire life cycle 61: 752-766Crossref (248) Scholar,84.Cao P. Oligonucleotide Array Database: expression.Rice. 2012; 17Crossref Scholar]66 Accessions [85.Zhao Q. al.Pan-genome highlights extent cultivated wild rice.Nat. 50: 278-284Crossref (149) Scholar]Soybean(Glycine max)120.5333.7973[86.Schmutz al.Genome palaeopolyploid soybean.Nature. 463: 7278Crossref (2570) Scholar]SoySNP50K [87.Song SoySNP50K, high-density soybean.PLoS 8e54985Crossref (292) Scholar]SoyaSNP180K [88.Lee Y.G. al.Development, validation soybean array.Plant 81: 625-636Crossref (30) Scholar]SoyKB [89.Joshi T. al.Soybean knowledge base (SoyKB): web resource integration translational genomics breeding.Nucleic 42: D1245-D1252Crossref Scholar]55 616 [90.Libault M. transcriptome model Glycine max, plants.Plant 63: 86-99PubMed Scholar]26 [91.Liu soybeans.Cell. 182: 162-176Abstract (42) Scholar]Barley(Hordeum vulgare)51.1158.94980 [92.International Barley A physical, functional barley 491: 711-716Crossref (978) Scholar]; 4790 [93.Mascher chromosome conformation capture ordered 544: 427-433Crossref (553) Scholar]9K Illumina Custom Genotyping [94.Comadr`an al.Natural homolog Antirrhinum CENTRORADIALIS contributed spring growth habit environmental adaptation barley.Nat. 44: 1388-1392Crossref (284) 50K [95.Bayer M.M. 50k array.Front. 8: 1792Crossref (74) Scholar]BarleyVarDB [96.Tan al.BarleyVarDB: variation.Database. 2020baaa091Crossref (1) Scholar]21 439 [97.Druka seed through development.Funct. Integr. 2006; 6: 202-211Crossref Scholar]20 [98.Jayakodi hidden legacy mutation breeding.Nature. 588: 284-289Crossref (6) Scholar]Sorghum(Sorghum bicolor)4057.9739 [99.Paterson A.H. Sorghum bicolor diversification grasses.Nature. 457: 551-556Crossref (1906) Scholar]3K [100.Bekele W.A. al.High-throughput sorghum: resequencing screening 11: 1112-1125Crossref (37) Scholar]SorGSD [101.Luo al.SorGSD: sorghum database.Biotechnol. Biofuels. 9: 6Crossref (21) Scholar]27 577 [102.Shakoor genotype-specific profiles vegetative tissues grain, sweet bioenergy sorghums.BMC 35Crossref (45) Scholar]n.d.Rapeseed(Brassica napus)3470.5849.7 [103.Chalhoub B. al.Early allopolyploid evolution post-Neolithic Brassica napus oilseed 345: 950-953Crossref (1027) Scholar]International (60K) [104.Clarke W.E. ancestral diploid species optimised markers allotetraploid genome.Theor. Appl. 129: 1887-1899Crossref Scholar]BnaGVD [105.Yan al.BnaGVD: rapeseed (Brassica napus).Plant Cell Physiol. 2021; (Published online January 5, 2021. https://doi.org/10.1093/pcp/pcaa169)Crossref Scholar]101 040 [106.Chao al.BrassicaEDB: crops.Int. Mol. 21: 5831Crossref (2) Scholar]8 [107.Song J.M. al.Eight reveal architecture ecotype differentiation napus.Nat. Plants. 34-45Crossref (61) Scholar]Dry beans(Phaseolus vulgaris)3328.9473 [108.Schmutz common bean dual domestications.Nat. 707-713Crossref (602) Scholar]BARCBean6K_1, BARCBean6K_2, BARCBean6K_3 [109.Song al.SNP assay map construction, anchoring sequence, other bean.G3 (Bethesda). 2285-2290Crossref (73) Scholar]PhaseolusGenes (http://phaseolusgenes.bioinformatics.ucdavis.edu/)[110.O'Rourke J.A. RNA-Seq bean.BMC 866Crossref (68) Scholar]n.d.Groundnut(Arachis hypogaea)29.648.82540 [111.Bertioli D.J. sequences Arachis duranensis ipaensis, ancestors peanut.Nat. 48: 438-446Crossref (372) 2540 [112.Zhuang peanut provides insight legume karyotypes, domestication.Nat. 51: 865-876Crossref (64) Scholar]'Axiom_Arachis' 58K [113.Pandey M.K. Axiom_Arachis 58 genetics groundnut.Sci. 7: 40577Crossref Scholar]n.d.57 344 Transcripts [114.Sinha al.Arachis hypogaea fastigiata subspecies groundnut accelerate applications.Plant 18: 2187-2200Crossref Scholar]n.d.Sugarcane(Saccharum officinarum)26.71949.3800–900 (Monoploid)76K [115.Yang X. al.Mining variations representative sugarcane accessions.BMC 594Crossref (17) 84K [116.Balsalobre T.W.A. al.GBS-based dosage QTL allow mining yield-related sugarcane.BMC 72Crossref Sugarcane100K [117.You construction identification.Theor. 13: 2829-2845Crossref Scholar]n.d.n.d.n.d.a Abbreviation: data.b Source: http://www.fao.org/faostat/en/#data/QC. Open table tab characterization underlying important agronomic processes. this article, discuss products delivered opportunities latest innovations offer sustain recent decades [i.e., or (GB)]. We highlight broad create selection. years, expedited timelines progress across range species, than 130 publicly bred different crops [5.Vogel Marker-Assisted Selection: Biotechnology Breeding Without Genetic Engineering. Greenpeace International, 2014Google majority noteworthy by variety programs include having elevated levels against diseases bacterial blight blast rust aestivum). Among biotic stresses, tolerance submergence, salinity, drought remained key target GAB. similar impact witnessed quality several (Box 1).Box 1Key Products Delivered Genomics-Assisted Some CropsGAB Biotic Stress ResistanceSimply inherited under influence strong-effect QTL, disease resistance, most preferred introgression approaches. 'Improved Samba Mahsuri' (ISM) carrying (BB) (Xanthomonas oryzae pv. oryzae) genes (Xa21, xa13, xa5) [132.Sundaram R.M. al.Marker assisted Mahsuri, elite indica variety.Euphytica. 160: 411-422Crossref Two major (Magnaporthe (Pi-2 Pi-54) BB (Xa38) further stacked 'ISM' [133.Madhavi K.R. background elite, resistant variety, Mahsuri.Euphytica. 212: 331-342Crossref (8) Scholar,134.Yugander al.Incorporation Xa38 Improved Mahsuri.PLoS 13e0198260Crossref (14) 'Pusa Basmati 1' pyramided two (Pi2+Pi5) (Pi54+Pi1+Pita) [135.Khanna near-isogenic gene(s) rice.Theor. 128: 1243-1259Crossref (57) version 1121' 6' (Pi2 Pi54) (xa13 Xa21) others [136.Ellur al.Improvement varieties marker backcross breeding.Plant 242: 330-341Crossref Scholar].A DNA improving stress response quality-related (http://maswheat.ucdavis.edu/protocols/index.htm). Examples versions hard red winter (HRWW) 'Jagger' 'Overley' Yr40/Lr57 Lr58, respectively [137.Kuraparthy V. PCR marker-assisted transfer leaf stripe Lr57 Yr40 wheats.Crop 49: 120-126Crossref 'HUW510' Lr34 [138.Vasistha al.Molecular validates spot blotch wheat.Euphytica. 213: 262Crossref (4) pearl millet, 'HHB 67-improved' represented downy mildew 67', which was released commercial cultivation India 2005 (see Rai al. [139.Rai K.N. al.Adaptation germplasm-derived parent millet.Plant Resour. Newsl. 154: 20-24Google Scholar]). Other success stories demonstrating cereal included eyespot (Rhizoctonia cerealis) Pch1, recessive rym4/ rym5 yellow mosaic viruses, mlo (Blumeria graminis f. sp. hordei).Unlike cereals, grain lagged behind terms product delivery; however, genotyping-based selections increasingly embraced For instance, pyramiding cyst nematode (Heterodera glycines) races (2, 3, 14) at USDA-ARS led registration high-yielding genotypes 'JTN 5503', 5303', 'DS 880', 5109' [140.Arelli al.Registration yielding JTN5503.Crop 2723-2724Crossref Scholar, 141.Arelli conventional JTN-4307 nematodes fungal diseases.J. Regist. 192-199Crossref 142.Arelli P.R. Young L.D. Inheritance PI 567516C LY1 infecting cv. Hartwig.Euphytica. 165: 1-4Crossref (19) 143.Smith USDA, ARS, National Program. Germplasm Information Network, 2010Google Similarly, Varshney [144.Varshney al.Marker-assisted region improve popular (Arachis L.).Theor. 127: 1771-1781Crossref (93) obtained set 20 hypogaea) showing yield increased (Puccinia arachidis) transferring susceptible ('ICGV 91114', 'JL 24', 'TAG 24'). chickpea, simultaneous wilt (Fusarium oxysporum ciceris) (Ascochyta rabiei) shown chickpea C 214 [145.Varshney backcrossing introgress Fusarium race 1 Ascochyta 214, chickpea.Plant Genome. 1-11Crossref (77) Scholar].GAB Abiotic ToleranceThe immense utility abiotic exemplified controlling submergence (sub1), salt (Saltol), introgressed them. Sub1 'Swarna', India, within short span 2 [146.Neeraja approach developing submergence-tolerant cultivars.Theor. 2007; 115: 767-776Crossref (276) Vietnam, nearly ten cross OM1490/IR64-Sub1 90–99% revival field conditions [147.Lang N.T. (MAB) Mekong delta.Omonrice. 11-21Google Higher survival rates mega-varieties, including 'Samba (BPT 5204), 'CR 1009' 'Thadokkham (TDK1) Laos, 'BR 11' Bangladesh also evident following QTL-introgression Hasan [148.Hasan backcrossing: useful method improvement.Biotechnol. Equip. 29: 237-254Crossref Scholar]).The Saltol various countries, candidate 1121', 6', 'AS 996', 'BT 7', 'Bacthom 'Q5DB', 'BRRI-Dhan 49' Waziri [149.Waziri al.Saltol salinity rice.Austin. Bioeng. 1-5Google Successful Sub1, Saltol, (Pi2, Pi9), gall midge (Orseolia (Gm1, Gm4) Tapaswini', pyramid (Xa 4, xa5, highly 'Tapaswini', demonstrated [150.Das G. al.Improved Tapaswini four six genes/QTLs, resistance/tolerance stresses 2413Crossref Scholar].Similar above-mentioned examples tolerance, major-effect QTLs 'Sabitri' (a yet drought-susceptible Nepal) yielded variants good type rain-fed areas Nepal countries South Asia [151.Dixit develop drought-tolerant Sabitri, Nepal.Euphytica. 184Crossref (11) availability stable effects facilitated well. 'QTL hotspot' 372' pulse 10216' (https://icar.org.in/content/development-two-superior-chickpea-varieties-genomics-assisted-breeding).GAB Quality TraitsOne breakthroughs plants involves introduction Gpc-B1 (grain protein content) tetra caused creation GPC viz. USA ('Farnum', 'Lassik', 'Westmore', 'Desert King-High Protein'), Canada ('Lillian', 'Somerset', 'Burnside'), Australia (improved 'Wyalkatchem', 'Gladius', 'VR 1128') Mitrofanova Khakimova [152.Mitrofanova O.P. A.G. New content.Russ. 477-487Crossref references therein). variant badh2 Wx basmati 'Manawthukha' (an Myanmar) resulted fragrance intermediate amylose content [153.Yi cooking Myanmar Manawthukha.Field Crops 113: 178-186Crossref By reducing cycles up 3 Chu [154.Chu oleic peanut.Plant 4: 110-117Crossref developed 'Tifguard High O/L' acid resistance. More recently, oil combined late (Phaeoisariopsis personata Berk. & Curtis) [155.Janila fatty desaturase mutant (ahFAD2A ahFAD2B) enhances low containing genotypes.Plant 203-213Crossref (66) Scholar,156.Yaduru Indian foliar SSR backcrossing.Crop 1-15Crossref (5) Resistance Simply bl
Language: Английский
Citations
372
Nature Plants, Journal Year: 2019, Volume and Issue: 5(9), P. 965 - 979
Published: Sept. 9, 2019
Language: Английский
Citations
270
Current Opinion in Plant Biology, Journal Year: 2020, Volume and Issue: 56, P. 190 - 196
Published: Jan. 28, 2020
Here we propose a 5G breeding approach for bringing much-needed disruptive changes to crop improvement. These 5Gs are Genome assembly, Germplasm characterization, Gene function identification, Genomic (GB), and editing (GE). In our view, it is important have genome assemblies available each deep collection of germplasm characterized at sequencing agronomic levels identification marker-trait associations superior haplotypes. Systems biology sequencing-based mapping approaches can be used identify genes involved in pathways leading the expression trait, thereby providing diagnostic markers target traits. genes, markers, haplotypes, genome-wide data may utilized GB GE methodologies combination with rapid cycle strategy.
Language: Английский
Citations
193
Science, Journal Year: 2023, Volume and Issue: 379(6635), P. 892 - 901
Published: March 2, 2023
We elucidate grapevine evolution and domestication histories with 3525 cultivated wild accessions worldwide. In the Pleistocene, harsh climate drove separation of grape ecotypes caused by continuous habitat fragmentation. Then, occurred concurrently about 11,000 years ago in Western Asia Caucasus to yield table wine grapevines. The domesticates dispersed into Europe early farmers, introgressed ancient western ecotypes, subsequently diversified along human migration trails muscat unique ancestries late Neolithic. Analyses traits also reveal new insights selection for berry palatability, hermaphroditism, flavor, skin color. These data demonstrate role grapevines inception agriculture across Eurasia.
Language: Английский
Citations
153
Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 120(24)
Published: June 5, 2023
Domesticated grapevines spread to Europe around 3,000 years ago. Previous studies have revealed genomic signals of introgression from wild cultivated grapes in Europe, but the time, mode, pattern, and biological effects these events not been investigated. Here, we studied resequencing data 345 samples spanning distributional range (Vitis vinifera ssp. sylvestris) (V. vinifera) grapes. Based on machine learning-based population genetic analyses, detected evidence for a single domestication grapevine, followed by continuous gene flow between European (EU) over past ~2,000 y, especially EU wine We also inferred that soft-selective sweeps were dominant artificial selection. Gene pathways associated with synthesis aromatic compounds enriched regions both selected introgressed, suggesting an important resource improving flavor Despite potential benefits grape improvement, introgressed fragments introduced higher deleterious burden, most SNPs structural variants hidden heterozygous state. Cultivated benefited adaptive grapes, has increased load. In general, our study beneficial harmful is critical breeding grapevine take advantage resources.
Language: Английский
Citations
45
PLANT PHYSIOLOGY, Journal Year: 2024, Volume and Issue: 195(2), P. 1401 - 1413
Published: Jan. 29, 2024
Abstract Plant domestication are evolutionary experiments conducted by early farmers since thousands years ago, during which the crop wild progenitors artificially selected for desired agronomic traits along with dramatic genomic variation in course of moderate to severe bottlenecks. However, previous investigations mainly focused on small-effect variants, while changes gene contents rarely investigated due lack population-level assemblies both and its relatives. Here, we applied comparative analyses discover gain loss grapevine using long-read representative population samples domesticated grapevines (V. vinifera ssp. vinifera) their sylvestris). Only ∼7% families were shared 16 Vitis genomes ∼8% specific each accession, suggesting variations genomes. Compared progenitors, accessions exhibited an increased presence genes associated asexual reproduction, showcased a higher abundance related pollination, revealing transition from sexual reproduction clonal propagation processes. Moreover, harbored fewer disease-resistance than progenitors. The SVs occurred frequently aroma between indicating rapid diversification these domestication. Our study provides insights resources biological studies breeding programs grapevine.
Language: Английский
Citations
18
Ecology and Evolution, Journal Year: 2019, Volume and Issue: 10(1), P. 579 - 589
Published: Dec. 7, 2019
Abstract A common goal of population genomics and molecular ecology is to reconstruct the demographic history a species interest. pair powerful tools based on sequentially Markovian coalescent have been developed infer past sizes using genome sequences. These methods are most useful when sequences available for only limited number genomes aim study ancient events. The results these analyses can be difficult interpret accurately, because doing so requires some understanding their theoretical basis sensitivity confounding factors. In this practical review, we explain key concepts underpinning pairwise multiple (PSMC MSMC, respectively). We relate use interpretation methods, how choice different parameter values by user affect accuracy precision inferences. Based our survey 100 PSMC studies 30 MSMC studies, describe two used in practice. Readers article will become familiar with principles, practice, inferring history.
Language: Английский
Citations
118
Nature Communications, Journal Year: 2020, Volume and Issue: 11(1)
Published: Sept. 8, 2020
Sustainable food production in the context of climate change necessitates diversification agriculture and a more efficient utilization plant genetic resources. Fonio millet (Digitaria exilis) is an orphan African cereal crop with great potential for dryland agriculture. Here, we establish high-quality genomic resources to facilitate fonio improvement through molecular breeding. These include chromosome-scale reference assembly deep re-sequencing 183 cultivated wild Digitaria accessions, enabling insights into diversity, population structure, domestication. diversity shaped by climatic, geographic, ethnolinguistic factors. Two genes associated seed size shattering showed signatures selection. Most known domestication from other models however have not experienced strong selection fonio, providing direct targets rapidly improve this hot dry environments.
Language: Английский
Citations
91
Australian Journal of Grape and Wine Research, Journal Year: 2020, Volume and Issue: 27(1), P. 8 - 25
Published: Dec. 8, 2020
Viticulture is facing emerging challenges not only because of the effect climate change on yield and composition grapes, but also a social demand for environmental-friendly agricultural management. Adaptation to these essential guarantee sustainability viticulture. The aim this review present adaptation possibilities from soil-hidden, often disregarded, part grapevine, roots. complexity soil–root interactions makes necessary comprehensive approach taking into account physiology, pathology genetics, in order outline strategies improve viticulture current future threats. Rootstocks are link between soil scion grafted crops, they have played an role since introduction phylloxera Europe at end 19th century. This outlines that threatening wine sector relevant rootstocks can play face We describe how along with management be exploited as tool deal effects soil-borne pests pathogens. Moreover, we discuss limitations diverse genetic rootstock breeding.
Language: Английский
Citations
80
Frontiers in Genetics, Journal Year: 2020, Volume and Issue: 11
Published: June 5, 2020
High-throughput genotyping is boosting genome-wide association studies (GWAS) in crop species, ultimately leading to the identification of single nucleotide polymorphisms (SNPs) and genes associated with economically important traits. Choosing a cost-effective method for GWAS requires careful examination several aspects, namely purpose scale study, crop-specific genomic features, technical economic matters each option. Once genotypic data have been obtained, quality control (QC) procedures must be applied avoid bias false signals genotype-phenotype tests. QC human has extensively reviewed, however may require different actions, depending on mating system breeding activities. Here we review most popular methods based next generation sequencing (NGS) array hybridization, provide observations that should guide investigator choice GWAS. We define best practises perform QC, including actions are specific species. Finally, an overview bioinformatics tools can used accomplish all needed tasks. Overall, this work aims guidelines harmonize those SNP datasets ready
Language: Английский
Citations
78