scholarly journals Genomic Approaches for Understanding Virulence and Resistance in the Sunflower-Orobanche Host-Parasite Interaction

2011 ◽  
Author(s):  
Daniel M. Joel ◽  
Steven J. Knapp ◽  
Yaakov Tadmor
Keyword(s):  
Genetic Mapping ◽  
Ssr Markers ◽  
High Throughput ◽  
Dna Markers ◽  
Snp Array ◽  
Snp Markers ◽  
R Genes ◽  
Draft Sequence ◽  
Mediterranean Countries ◽  
Sunflower Genome

Oroginal Objectives: (i) identify DNA markers linked to the avirulence (Avr) locus and locate the Avr locus through genetic mapping with an inter-race Orobanche cumana population; (ii) develop high-throughput fingerprint DNA markers for genotypingO. cumana races; (iii) identify nucleotide binding domain leucine rich repeat (NB-LRR) genes encoding R proteins conferring resistance to O. cumana in sunflower; (iv) increase the resolution of the chromosomal segment harboring Or₅ and related R genes through genetic and physical mapping in previously and newly developed mapping populations of sunflower; and (v) develop high-throughput DNA markers for rapidly and efficiently identifying and transferring sunflower R genes through marker-assisted selection. Revisions made during the course of project: Following changes in O. cumana race distribution in Israel, the newly arrived virulent race H was chosen for further analysis. HA412-HO, which was primarily chosen as a susceptible sunflower cultivar, was more resistant to the new parasite populations than var. Shemesh, thus we shifted sunflower research into analyzing the resistance of HA412-HO. We exceeded the deliverables for Objectives #3-5 by securing funding for complete physical and high-density genetic mapping of the sunflower genome, in addition to producing a complete draft sequence of the sunflower genome. We discovered limited diversity between the parents of the O. cumana population developed for the mapping study. Hence, the developed DNA marker resources were insufficient to support genetic map construction. This objective was beyond the scale and scope of the funding. This objective is challenging enough to be the entire focus of follow up studies. Background to the topic: O. cumana, an obligate parasitic weed, is one of the most economically important and damaging diseases of sunflower, causes significant yield losses in susceptible genotypes, and threatens production in Israel and many other countries. Breeding for resistance has been crucial for protecting sunflower from O. cumana, and problematic because new races of the pathogen continually emerge, necessitating discovery and deployment of new R genes. The process is challenging because of the uncertainty in identifying races in a genetically diverse parasite. Major conclusions, solutions, achievements: We developed a small collection of SSR markers for genetic mapping in O. cumana and completed a diversity study to lay the ground for objective #1. Because DNA sequencing and SNPgenotyping technology dramatically advanced during the course of the study, we recommend shifting future work to SNP discovery and mapping using array-based approaches, instead of SSR markers. We completed a pilot study using a 96-SNP array, but it was not large enough to support genetic mapping in O.cumana. The development of further SNPs was beyond the scope of the grant. However, the collection of SSR markers was ideal for genetic diversity analysis, which indicated that O. cumanapopulations in Israel considerably differ frompopulations in other Mediterranean countries. We supplied physical and genetic mapping resources for identifying R-genes in sunflower responsible for resistance to O. cumana. Several thousand mapped SNP markers and a complete draft of the sunflower genome sequence are powerful tools for identifying additional candidate genes and understanding the genomic architecture of O. cumana-resistanceanddisease-resistance genes. Implications: The OrobancheSSR markers have utility in sunflower breeding and genetics programs, as well as a tool for understanding the heterogeneity of races in the field and for geographically mapping of pathotypes.The segregating populations of both Orobanche and sunflower hybrids are now available for QTL analyses.

Mapping QTL Associated with Partial Resistance to Aphanomyces Root rot in Pea (Pisum Sativum L.) using a 13.2K SNP Array and SSR Markers

2021 ◽  
Author(s):  
Longfei Wu ◽  
Rudolph Fredua-Agyeman ◽  
Sheau-Fang Hwang ◽  
Kan-Fa Chang ◽  
Robert Conner ◽  
...  
Keyword(s):  
Pisum Sativum ◽  
Ssr Markers ◽  
Root Rot ◽  
Partial Resistance ◽  
Snp Array ◽  
Snp Markers ◽  
Minor Effect ◽  
Aphanomyces Euteiches ◽  
Phenotypic Data ◽  
Soilborne Disease

Abstract Aphanomyces root rot (ARR), caused by Aphanomyces euteiches Drechs., is a destructive soilborne disease of field pea (Pisum Sativum L.). No completely resistant pea germplasm is available, and current ARR management strategies rely on partial resistance and fungicidal seed treatments. In this study, an F8 recombinant inbred line (RIL) population of 135 individuals from the cross ‘Reward’ (susceptible) × ‘00-2067’ (tolerant) was evaluated for reaction to ARR under greenhouse conditions with the A. euteiches isolate Ae-MDCR1 and over 2 years in a field nursery in Morden, Manitoba. Root rot severity, foliar weight, plant vigor and height were used as estimates of tolerance to ARR. Genotyping was conducted with a 13.2K single-nucleotide polymorphism (SNP) array and 222 simple sequence repeat (SSR) markers. Statistical analyses of the phenotypic data indicated significant (P<0.001) genotypic effects and significant G×E interactions (P<0.05) in all experiments. After filtering, 3050 (23.1%) of the SNP and 30 (13.5%) of the SSR markers were retained for linkage analysis, which distributed 2999 (2978 SNP + 21 SSR) of the markers onto nine linkage groups representing the seven chromosomes of pea. Mapping of quantitative trait loci (QTL) identified 5 major-effect (R2 > 20%), 13 moderate-effect (10%<R2< 20%) effect and 10 minor-effect (R2 <10%) QTL. A genomic region on chromosome IV, delimited by the SNP markers PsCam037549_22628_1642 and PsCam026054_14999_2864, was identified as the most consistent region responsible for partial resistance to A. euteiches isolate Ae-MDCR1. Other genomic regions important for resistance were of the order chromosome III, II and VII.

LEGITIMACY OF PROGENIES USING SSR MARKERS AS CONTROLLING SYSTEM AND EARLIER SELECTION IN THE OIL PALM NURSERY (Elaeis guineensis JACQ.)

2018 ◽  
Vol 25 (1) ◽  
pp. 21-30
Author(s):  
Rokhana Faizah ◽  
Sri Wening ◽  
Abdul Razak Purba
Keyword(s):  
Dna Fingerprinting ◽  
Ssr Markers ◽  
Oil Palm ◽  
Dna Markers ◽  
Elaeis Guineensis ◽  
Gene Marker ◽  
Controlling System ◽  
Crossing Probability ◽  
Simple Sequence

Information of legitimacy of oil palm progenies is important to guaranty the quality and to control commercial seeds procedures. A true and legitimate cross will produce progeny which has a combination of their parent's allele. The information could be obtained early in the nursery stage through DNA fingerprinting analysis. Simple Sequence Repeats (SSR) is one of DNA markers used for DNA fingerprinting, since the marker system has advantages to acquire information of allele per individual in population and efficiency diverse allele of progeny and their parents. The aim of the research is to obtain legitimacy of 12 progenies analyzing in the oil palm nursery stage. Thirteen SSR markers were used to analyze 12 crossings number of oil palm. The genotypes data by alleles of SSR inferred and quantified using Gene Marker® Software version 2.4.0 Soft Genetics® LLC and analyzed based on Mendel's Law of Segregation. The result showed based on heredity pattern of progeny and their parent's allele that progenies H were indicated genetically derived from their known parents while progenies from A and G indicated as illegitimate crossing. Probability value for legitimacy of progenies of 9 other crosses has 0.031 and 0.5. Legitimacy analysis of progeny using SSR markers could be used to control the quality of crossing material and earlier selection in the oil palm nursery.

scholarly journals Next generation genome-wide association tool: Design and coverage of a high-throughput European-optimized SNP array

Genomics ◽  
2011 ◽  
Vol 98 (2) ◽  
pp. 79-89 ◽  
Author(s):  
Thomas J. Hoffmann ◽  
Mark N. Kvale ◽  
Stephanie E. Hesselson ◽  
Yiping Zhan ◽  
Christine Aquino ◽  
...  
Keyword(s):  
High Throughput ◽  
Snp Array ◽  
Tool Design ◽  
Genome Wide Association ◽  
Next Generation ◽  
Genome Wide

High-throughput genetic mapping in Arabidopsis thaliana

1999 ◽  
Vol 261 (2) ◽  
pp. 408-415 ◽  
Author(s):  
M. R. Ponce ◽  
P. Robles ◽  
J. L. Micol
Keyword(s):  
Arabidopsis Thaliana ◽  
Genetic Mapping ◽  
High Throughput

Genetic mapping of linkage group XIX and identification of sex-linked SSR markers in a Populus tremula × Populus tremuloides cross

2011 ◽  
Vol 41 (2) ◽  
pp. 245-253 ◽  
Author(s):  
Birte Pakull ◽  
Katrin Groppe ◽  
Federica Mecucci ◽  
Muriel Gaudet ◽  
Maurizio Sabatti ◽  
...  
Keyword(s):  
Linkage Group ◽  
Genetic Mapping ◽  
Ssr Markers ◽  
Genome Sequence ◽  
Populus Tremuloides ◽  
Populus Trichocarpa ◽  
Interspecific Cross ◽  
Populus Tremula ◽  
Central Position ◽  
Populus Alba

A progeny of 130 F1 individuals of an interspecific cross between Populus tremula L. and Populus tremuloides Michx. was used for genetic mapping of linkage group XIX with SSR markers based on the Populus trichocarpa Torr. & A. Gray genome sequence. Several fully sex-linked SSR markers were identified and mapped to a central position on the male P. tremuloides map of linkage group XIX. For the SSR markers tested here, the position on the assembled P. trichocarpa genome sequence is known, allowing sex-linked markers to be assigned to the central region of scaffold/chromosome 19 of P. trichocarpa. The sex linkage of the SSR markers was validated in other P. tremula × P. tremuloides crosses and also tested in Populus alba L. and Populus nigra L.

scholarly journals Combining Single Nucleotide Polymorphism Genotyping Array with Bulked Segregant Analysis to Map a Gene Controlling Adult Plant Resistance to Stripe Rust in Wheat Line 03031-1-5 H62

2018 ◽  
Vol 108 (1) ◽  
pp. 103-113 ◽  
Author(s):  
Jianhui Wu ◽  
Qilin Wang ◽  
Liangsheng Xu ◽  
Xianming Chen ◽  
Bei Li ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Stripe Rust ◽  
Rust Resistance ◽  
Bulked Segregant Analysis ◽  
Snp Array ◽  
Adult Plant ◽  
Wheat Line ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Kasp Markers

Stripe rust, caused by Puccinia striiformis f. sp. tritici, is one of the most devastating diseases of wheat worldwide. Growing resistant cultivars is considered the best approach to manage this disease. In order to identify the resistance gene(s) in wheat line 03031-1-5 H62, which displayed high resistance to stripe rust at adult plant stage, a cross was made between 03031-1-5 H62 and susceptible cultivar Avocet S. The mapping population was tested with Chinese P. striiformis f. sp. tritici race CYR32 through artificial inoculation in a field in Yangling, Shaanxi Province and under natural infection in Tianshui, Gansu Province. The segregation ratios indicated that the resistance was conferred by a single dominant gene, temporarily designated as YrH62. A combination of bulked segregant analysis (BSA) with wheat 90K single nucleotide polymorphism (SNP) array was used to identify molecular markers linked to YrH62. A total of 376 polymorphic SNP loci identified from the BSA analysis were located on chromosome 1B, from which 35 kompetitive allele-specific PCR (KASP) markers selected together with 84 simple sequence repeat (SSR) markers on 1B were used to screen polymorphism and a chromosome region associated with rust resistance was identified. To saturate the chromosomal region covering the YrH62 locus, a 660K SNP array was used to identify more SNP markers. To develop tightly linked markers for marker-assisted selection of YrH62 in wheat breeding, 18 SNPs were converted into KASP markers. A final linkage map consisting of 15 KASP and 3 SSR markers was constructed with KASP markers AX-109352427 and AX-109862469 flanking the YrH62 locus in a 1.0 cM interval. YrH62 explained 63.8 and 69.3% of the phenotypic variation for disease severity and infection type, respectively. YrH62 was located near the centromeric region of chromosome 1BS based on the positions of the SSR markers in 1B deletion bins. Based on the origin, responses to P. striiformis f. sp. tritici races, and marker distances, YrH62 is likely different from the other reported stripe rust resistance genes/quantitative trait loci on 1B. The gene and tightly linked KASP markers will be useful for breeding wheat cultivars with resistance to stripe rust.

scholarly journals Investigation of Genetic Relationships within Miscanthus using SNP Markers Identified using SLAF-Seq

2021 ◽  
Author(s):  
ZHIYONG Chen ◽  
Yancen He ◽  
Yasir Iqbal ◽  
Yanlan Shi ◽  
Hongmei Huang ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Genetic Relationships ◽  
Female Parent ◽  
Snp Markers ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Sequencing Method ◽  
Specific Locus

Abstract Background: Miscanthus, which is a leading dedicated-energy grass in Europe and in parts of Asia, is expected to play a key role in the development of the future bioeconomy. However, due to its complex genetic background, it is difficult to investigate phylogenetic relationships and the evolution of gene function in this genus. Here, we investigated 50 Miscanthus germplasms: 1 female parent (M. lutarioriparius), 30 candidate male parents (M. lutarioriparius, M. sinensis, and M. sacchariflorus), and 19 offspring. We used high-throughput Specific-Locus Amplified Fragment sequencing (SLAF-seq) to identify informative single nucleotide polymorphisms (SNPs) in all germplasms.Results: We identified 800,081 SLAF tags, of which 160,368 were polymorphic. Each tag was 264–364 bp long. The obtained SNPs were used to investigate genetic relationships within Miscanthus. We constructed a phylogenetic tree of the 50 germplasms using the obtained SNPs, and found that the germplasms fell into two clades: one clade of M. sinensis only and one clade that included the offspring, M. lutarioriparius, and M. sacchariflorus. Genetic cluster analysis indicated that M. lutarioriparius germplasm C3 was the most likely male parent of the offspring.Conclusions: As a high-throughput sequencing method, SLAF-seq can be used to identify informative SNPs in Miscanthus germplasms and to rapidly characterize genetic relationships within this genus. Our results will support the development of breeding programs utilizing Miscanthus cultivars with elite biomass- or fiber-production potential.

scholarly journals Precision phenotyping reveals novel loci for quantitative resistance to septoria tritici blotch in European winter wheat

2018 ◽  
Author(s):  
Steven Yates ◽  
Alexey Mikaberidze ◽  
Simon Krattinger ◽  
Michael Abrouk ◽  
Andreas Hund ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Winter Wheat ◽  
High Throughput ◽  
Quantitative Resistance ◽  
Small Chromosome ◽  
Snp Markers ◽  
Automated Image Analysis ◽  
Septoria Tritici Blotch ◽  
Septoria Tritici ◽  
Limiting Factor

Accurate, high-throughput phenotyping for quantitative traits is the limiting factor for progress in plant breeding. We developed automated image analysis to measure quantitative resistance to septoria tritici blotch (STB), a globally important wheat disease, enabling identification of small chromosome intervals containing plausible candidate genes for STB resistance. 335 winter wheat cultivars were included in a replicated field experiment that experienced natural epidemic development by a highly diverse but fungicide-resistant pathogen population. More than 5.4 million automatically generated phenotypes were associated with 13,648 SNP markers to perform a GWAS. We identified 26 chromosome intervals explaining 1.9-10.6% of the variance associated with four resistance traits. Seventeen of the intervals were less than 5 Mbp in size and encoded only 173 genes, including many genes associated with disease resistance. Five intervals contained four or fewer genes, providing high priority targets for functional validation. Ten chromosome intervals were not previously associated with STB resistance. Our experiment illustrates how high-throughput automated phenotyping can accelerate breeding for quantitative disease resistance. The SNP markers associated with these chromosome intervals can be used to recombine different forms of quantitative STB resistance that are likely to be more durable than pyramids of major resistance genes.

scholarly journals Structure and Migration in U.S. Blumeria graminis f. sp. tritici Populations

2016 ◽  
Vol 106 (3) ◽  
pp. 295-304 ◽  
Author(s):  
Christina Cowger ◽  
Ryan Parks ◽  
Evsey Kosman
Keyword(s):  
Ssr Markers ◽  
Large Scale ◽  
Isolation By Distance ◽  
Blumeria Graminis ◽  
Snp Markers ◽  
Eastern United States ◽  
Long Distance ◽  
Continental Scale ◽  
South Central ◽  
Haplotypic Diversity

While wheat powdery mildew occurs throughout the south-central and eastern United States, epidemics are especially damaging in the Mid-Atlantic states. The structure of the U.S. Blumeria graminis f. sp. tritici population was assessed based on a sample of 238 single-spored isolates. The isolates were collected from 16 locations in 12 states (18 site-years) as chasmothecial samples in 2003 or 2005, or as conidial samples in 2007 or 2010. DNA was evaluated using nine single nucleotide polymorphism (SNP) markers in four housekeeping genes, and 10 simple sequence repeat (SSR) markers. The SSR markers were variably polymorphic, with allele numbers ranging from 3 to 39 per locus. Genotypic diversity was high (210 haplotypes) and in eight of the site-years, every isolate had a different SSR genotype. SNP haplotypic diversity was lower; although 15 haplotypes were identified, the majority of isolates possessed one of two haplotypes. The chasmothecial samples showed no evidence of linkage disequilibrium (P = 0.36), while the conidial samples did (P = 0.001), but the two groups had nearly identical mean levels of genetic diversity, which was moderate. There was a weakly positive relationship between genetic distance and geographic distance (R2 = 0.25, P = 0.001), indicating modest isolation by distance. Most locations in the Mid-Atlantic and Great Lakes regions clustered together genetically, while Southeast locations formed a distinct but adjacent cluster; all of these were genetically separated from Southern Plains locations and an intermediate location in Kentucky. One-way migration was detected at a rate of approximately five individuals per generation from populations west of the Appalachian Mountains to those to the east, despite the fact that the Atlantic states experience more frequent and damaging wheat mildew epidemics. Overall, the evidence argues for a large-scale mosaic of overlapping populations that re-establish themselves from local sources, rather than continental-scale extinction and re-establishment, and a low rate of long-distance dispersal roughly from west to east, consistent with prevailing wind directions.

scholarly journals Development of maizeSNP3072, a high-throughput compatible SNP array, for DNA fingerprinting identification of Chinese maize varieties

2015 ◽  
Vol 35 (6) ◽  
Author(s):  
Hong-Li Tian ◽  
Feng-Ge Wang ◽  
Jiu-Ran Zhao ◽  
Hong-Mei Yi ◽  
Lu Wang ◽  
...  
Keyword(s):  
Dna Fingerprinting ◽  
High Throughput ◽  
Snp Array ◽  
Maize Varieties
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