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| 1 | A High-Throughput Phenotyping System Using Machine Vision to Quantify Severity of Grapevine Powdery Mildew显示文摘Powdery mildews present specific challenges to phenotyping systems that are based on imaging.Having previously developed lowthroughput,quantitative microscopy approaches for phenotyping resistance to Erysiphe necator on thousands of grape leaf disk samples for genetic analysis,here we developed automated imaging and analysis methods for E.necator severity on leaf disks.By pairing a 46-megapixel CMOS sensor camera,a long-working distance lens providing 3.5×magnification,X-Y sample positioning,and Z-axis focusing movement,the system captured 78%of the area of a 1-cm diameter leaf disk in 3 to 10 focus-stacked images within 13.5 to 26 seconds.Each image pixel represented 1.44 m2 of the leaf disk.A convolutional neural network(CNN)based on GoogLeNet determined the presence or absence of E.necator hyphae in approximately 800 subimages per leaf disk as an assessment of severity,with a training validation accuracy of 94.3%.For an independent image set the CNN was in agreement with human experts for 89.3%to 91.7%of subimages.This live-imaging approach was nondestructive,and a repeated measures time course of infection showed differentiation among susceptible,moderate,and resistant samples.Processing over one thousand samples per day with good accuracy,the system can assess host resistance,chemical or biological efficacy,or other phenotypic responses of grapevine to E.necator.In addition,new CNNs could be readily developed for phenotyping within diverse pathosystems or for diverse traits amenable to leaf disk assays. | Andrew Bierman Tim LaPlumm Lance Cadle-Davidson David Gadoury Dani Martinez Surya Sapkota Mark Rea | 2019 | Plant Phenomics2019，1，1： | 4 |
| 2 | A next-generation marker genotyping platform(AmpSeq)in heterozygous crops:a case study for marker-assisted selection in grapevine显示文摘Marker-assisted selection(MAS)is often employed in crop breeding programs to accelerate and enhance cultivar development,via selection during the juvenile phase and parental selection prior to crossing.Next-generation sequencing and its derivative technologies have been used for genome-wide molecular marker discovery.To bridge the gap between marker development and MAS implementation,this study developed a novel practical strategy with a semi-automated pipeline that incorporates trait-associated single nucleotide polymorphism marker discovery,low-cost genotyping through amplicon sequencing(AmpSeq)and decision making.The results document the development of a MAS package derived from genotyping-by-sequencing using three traits(flower sex,disease resistance and acylated anthocyanins)in grapevine breeding.The vast majority of sequence reads(⩾99%)were from the targeted regions.Across 380 individuals and up to 31 amplicons sequenced in each lane of MiSeq data,most amplicons(83 to 87%)had<10%missing data,and read depth had a median of 220–244×.Several strengths of the AmpSeq platform that make this approach of broad interest in diverse crop species include accuracy,flexibility,speed,high-throughput,low-cost and easily automated analysis. | Shanshan Yang Jonathan Fresnedo-Ramíre Minghui Wang Linda Cote Peter Schweitzer Paola Barba Elizabeth M Takacs Matthew Clark James Luby David C Manns Gavin Sacks Anna Katharine Mansfield Jason Londo Anne Fennell David Gadoury Bruce Reisch Lance Cadle-Davidson Qi Sun | 2016 | Horticulture Research2016，3，1： | 2 |
| 3 | Discovery and genome-guided mapping of REN12 from Vitis amurensis, conferring strong, rapid resistance to grapevine powdery mildew显示文摘Powdery mildew resistance genes restrict infection attempts at different stages of pathogenesis.Here,a strong and rapid powdery mildew resistance phenotype was discovered from Vitis amurensis‘PI 588631’that rapidly stopped over 97%of Erysiphe necator conidia,before or immediately after emergence of a secondary hypha from appressoria.This resistance was effective across multiple years of vineyard evaluation on leaves,stems,rachises,and fruit and against a diverse array of E.necator laboratory isolates.Using core genome rhAmpSeq markers,resistance mapped to a single dominant locus(here named REN12)on chromosome 13 near 22.8–27.0 Mb,irrespective of tissue type,explaining up to 86.9%of the phenotypic variation observed on leaves.Shotgun sequencing of recombinant vines using skim-seq technology enabled the locus to be further resolved to a 780 kb region,from 25.15 to 25.93 Mb.RNASeq analysis indicated the allele-specific expression of four resistance genes(NLRs)from the resistant parent.REN12 is one of the strongest powdery mildew resistance loci in grapevine yet documented,and the rhAmpSeq sequences presented here can be directly used for marker-assisted selection or converted to other genotyping platforms.While no virulent isolates were identified among the genetically diverse isolates and wild populations of E.necator tested here,NLR loci like REN12 are often race-specific.Thus,stacking of multiple resistance genes and minimal use of fungicides should enhance the durability of resistance and could enable a 90%reduction in fungicides in low-rainfall climates where few other pathogens attack the foliage or fruit. | Surya Sapkota Cheng Zou Craig Ledbetter Anna Underhill Qi Sun David Gadoury Lance Cadle-Davidson | 2023 | Horticulture Research2023，10，5： | 0 |
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