Greenbug Schizaphis graminum (Rondani) is a major insect pest that significantly affects barley production worldwide. The identification of novel greenbug resistance genes is crucial for sustainable ...barley production and global food security. To identify greenbug resistance genes from a US breeding line PI 499276 and a Chinese cultivar PI 566459, two F6:7 recombinant inbred line (RIL) populations developed from crosses Weskan × PI 499276 and Weskan × PI 566459 were phenotyped for responses to greenbug biotype E and genotyped using genotyping‐by‐sequencing (GBS). Linkage analysis using single nucleotide polymorphism and kompetitive allele‐specific polymorphism (KASP) markers delimited the greenbug resistance genes from PI 499276 and PI 566459 to a 1.2 Mb genomic region between 666.5 and 667.7 Mb on the long arm of chromosome 3H in the Morex Hordeum vulgare r1 reference sequence. Allelism tests based on responses of four F2 populations to greenbug biotype E indicated that the greenbug resistance gene in PI 499276 and PI 566459 is either allelic or very close to Rsg1. Given that PI 499276 and PI 566459 shared the same unique resistance pattern to a set of 14 greenbug biotypes, which is different from those of other Rsg1 alleles, they carry a new Rsg1 allele. The greenbug resistance genes in Post 90, PI 499276/PI 566459, and WBDC 336 were designated as Rsg1.a1, Rsg1.a2, and Rsg1.a3, respectively. KASP markers KASP‐Rsg1a3‐1, KASP‐Rsg1a3‐2, and KASP160 can be used to tag Rsg1.a2 in barley breeding.
Core Ideas
A new Rsg1 allele, designated as Rsg1.a2, was identified in two barley accessions.
Rsg1.a2 confers resistance to multiple greenbug biotypes.
User‐friendly, high‐throughput kompetitive allele‐specific polymorphism (KASP) markers were developed to facilitate the use of Rsg1.a2 in barley breeding.
Greenbug (Schizaphis graminum Rondani) is a pest that poses a serious threat to cereal production worldwide. Yield losses caused by greenbug are predicted to increase because of global warming. To ...date, only a few barley (Hordeum vulgare L.) greenbug resistance genes have been reported and new genes are urgently needed because of the continuous occurrence of novel greenbug biotypes. PI 565676, a landrace collected from Henan province of China, exhibits high resistance to several predominant greenbug biotypes. An F6:7 recombinant inbred line (RIL) population derived from the cross PI 565676 × ‘Weskan’ was evaluated for response to greenbug biotypes E and F using a standard aphid assay protocol, and a randomized complete block design with two replicates was adopted. The RIL population was genotyped using single‐nucleotide polymorphisms (SNPs) markers generated by genotyping‐by‐sequencing (GBS). Gene mapping placed the greenbug resistance gene in PI 565676, designated Rsg3, to an interval of 93,140 bp between 667,558,306 and 667,651,446 bp on the long arm of chromosome 3H. Four high‐confidence genes were annotated in this region with one encoding a leucine‐rich repeat‐containing protein. An allelism test indicated that Rsg3 is independent of the Rsg1 locus, with estimated recombination frequency of 12.85 ± 0.20% and genetic distance of 13.14 ± 0.21 cM between the two loci. Therefore, Rsg3 represents a new locus for greenbug resistance. Two SNPs flanking Rsg3 were converted to Kompetitive Allele Specific PCR (KASP) markers, which can be used to tag Rsg3 in barley breeding.
Core Ideas
A new greenbug resistance gene, Rsg3, was mapped to the long arm of chromosome 3H in the Chinese barley landrace PI 565676.
Rsg3 was placed to an interval of <100 kb, in which four genes were annotated.
An allelism test indicated that Rsg3 is independent of the Rsg1 locus.
Two user‐friendly, high‐throughput KASP markers were developed to facilitate the use of Rsg3 in barley breeding.
Background Wheat (Triticum aestivum L.) is a staple food crop worldwide. The wheat genome has not yet been sequenced due to its huge genome size (approximately 17,000 Mb) and high levels of ...repetitive sequences; the whole genome sequence may not be expected in the near future. Available linkage maps have low marker density due to limitation in available markers; therefore new technologies that detect genome-wide polymorphisms are still needed to discover a large number of new markers for construction of high-resolution maps. A high-resolution map is a critical tool for gene isolation, molecular breeding and genomic research. Single feature polymorphism (SFP) is a new microarray-based type of marker that is detected by hybridization of DNA or cRNA to oligonucleotide probes. This study was conducted to explore the feasibility of using the Affymetrix GeneChip to discover and map SFPs in the large hexaploid wheat genome. Results: Six wheat varieties of diverse origins (Ning 7840, Clark, Jagger, Encruzilhada, Chinese Spring, and Opata 85) were analyzed for significant probe by variety interactions and 396 probe sets with SFPs were identified. A subset of 164 unigenes was sequenced and 54% showed polymorphism within probes. Microarray analysis of 71 recombinant inbred lines from the cross Ning 7840/Clark identified 955 SFPs and 877 of them were mapped together with 269 simple sequence repeat markers. The SFPs were randomly distributed within a chromosome but were unevenly distributed among different genomes. The B genome had the most SFPs, and the D genome had the least. Map positions of a selected set of SFPs were validated by mapping single nucleotide polymorphism using SNaPshot and comparing with expressed sequence tags mapping data. Conclusion: The Affymetrix array is a cost-effective platform for SFP discovery and SFP mapping in wheat. The new high-density map constructed in this study will be a useful tool for genetic and genomic research in wheat.
Core Ideas
Mapping of GBS reads of 398 accessions to the draft genome sequence identified 82,112 SNPs
Model‐based clustering analysis revealed a hierarchical genetic structure of six subgroups
...Greater LD decay in the west‐African subpopulation is likely due to long history of recombination
Genetic differentiation analysis among subpopulations revealed variation in selection signatures
Pearl millet Cenchrus americanus (L.) Morrone syn. Pennisetum glaucum (L.) R. Br. is one of the most extensively cultivated cereals in the world, after wheat (Triticum aestivum L.), maize (Zea mays L.), rice (Oryza sativa L.), barley (Hordeum vulgare L.), and sorghum Sorghum bicolor (L.) Moench. It is the main component of traditional farming systems and a staple food in the arid and semiarid regions of Africa and southern Asia. However, its genetic improvement is lagging behind other major cereals and the yield is still low. Genotyping‐by‐sequencing (GBS)‐based single‐nucleotide polymorphism (SNP) markers were screened on a total of 398 accessions from different geographic regions to assess genetic diversity, population structure, and linkage disequilibrium (LD). By mapping the GBS reads to the reference genome sequence, 82,112 genome‐wide SNPs were discovered. The telomeric regions of the chromosomes have the higher SNP density than in pericentromeric regions. Model‐based clustering analysis of the population revealed a hierarchical genetic structure of six subgroups that mostly overlap with the geographic origins or sources of the genotypes but with differing levels of admixtures. A neighbor‐joining phylogeny analysis revealed that germplasm from western Africa rooted the dendrogram with much diversity within each subgroup. Greater LD decay was observed in the west‐African subpopulation than in the other subpopulations, indicating a long history of recombination among landraces. Also, genome scan of genetic differentiatation detected different selection histories among subpopulations. These results have potential application in the development of genomic‐assisted breeding in pearl millet and heterotic grouping of the lines for improved hybrid performance.
Greenbug (Schizaphis graminum Rondani) is a destructive insect pest that not only damages plants, but also serves as a vector for many viruses. Host plant resistance is the preferred strategy for ...managing greenbug. Two greenbug resistance genes, Rsg1 and Rsg2, have been reported in barley. To breed cultivars with effective resistance against various greenbug biotypes, additional resistance genes are urgently needed to sustain barley production. Wild barley accession WBDC053 (PI 681777) was previously found to be resistant to several greenbug biotypes. In this study, a recombinant inbred line (RIL) population derived from Weskan × WBDC053 was evaluated for response to two greenbug biotypes (E and TX1) and genotyped using genotyping by sequencing (GBS). A set of 3347 high quality GBS-derived single nucleotide polymorphisms (SNPs) were then used to map the greenbug resistance gene in this wild barley accession. Linkage analysis placed the greenbug resistance gene in a 2.35 Mb interval (0–2,354,645 bp) in the terminal region of the short arm of chromosome 2H. This interval harbors 15 genes with leucine-rich-repeat (LRR) protein domains. An allelism test indicated that the greenbug resistance gene in WBDC053, designated Rsg2.a3, is likely allelic or closely linked to Rsg2. GBS-SNPs 2H_1318811 and 2H_1839499 co-segregating with Rsg2.a3 in the RIL population were converted to Kompetitive allele specific PCR (KASP) markers KASP-Rsg2.a3-1 and KASP-Rsg2.a3-2, respectively. The two KASP markers can be used to select Rsg2.a3 and have the potential to tag Rsg2 in barley improvement programs.
In the Southern Great Plains, wheat cultivars have been selected for a combination of outstanding yield and drought tolerance as a long-term breeding goal. To understand the underlying genetic ...mechanisms, this study aimed to dissect the quantitative trait loci (QTL) associated with yield components and kernel traits in two wheat cultivars `TAM 112' and `Duster' under both irrigated and dryland environments. A set of 182 recombined inbred lines (RIL) derived from the cross of TAM 112/Duster were planted in 13 diverse environments for evaluation of 18 yield and kernel related traits. High-density genetic linkage map was constructed using 5,081 single nucleotide polymorphisms (SNPs) from genotyping-by-sequencing (GBS). QTL mapping analysis detected 134 QTL regions on all 21 wheat chromosomes, including 30 pleiotropic QTL regions and 21 consistent QTL regions, with 10 QTL regions in common. Three major pleiotropic QTL on the short arms of chromosomes 2B (57.5 - 61.6 Mbps), 2D (37.1 - 38.7 Mbps), and 7D (66.0 - 69.2 Mbps) colocalized with genes
,
, and
, respectively. And four consistent QTL associated with kernel length (KLEN), thousand kernel weight (TKW), plot grain yield (YLD), and kernel spike
(KPS) (
,
,
, and
) explained more than 5% of the phenotypic variation. QTL Qklen.tamu.1A.325 is a novel QTL with consistent effects under all tested environments. Marker haplotype analysis indicated the QTL combinations significantly increased yield and kernel traits. QTL and the linked markers identified in this study will facilitate future marker-assisted selection (MAS) for pyramiding the favorable alleles and QTL map-based cloning.
Greenbug (Schizaphis graminum, Rondani) is a serious insect pest in many wheat growing regions and has been infesting cereal crops in the USA for over a century. Continuous occurrence of new greenbug ...biotypes makes it essential to explore all greenbug resistant sources available to manage this pest. Gb1, a recessive greenbug resistance gene in DS28A, confers resistance to several economically important greenbug biotypes and is the only gene found to be resistant to greenbug biotype F. A set of 174 F2:3 lines from the cross DS28A × Custer was evaluated for resistance to greenbug biotype F in 2020 and 2022. Selective genotyping of the corresponding F2 population using single nucleotide polymorphism (SNP) markers generated by genotyping-by-sequencing (GBS) led to the identification of a candidate genomic region for Gb1. Thus, SSR markers previously mapped in this region were used to genotype the entire F2 population, and kompetitive allele specific PCR (KASP) markers were also developed from SNPs in the target region. Gb1 was placed in the terminal region of the short arm of chromosome 1A, and its location was confirmed in a second population derived from the cross DS28A × PI 697274. The combined data analysis from the two mapping populations delimited Gb1 to a < 1 Mb interval between 13,328,200 and 14,241,426 bp on 1AS.
Spring wheat (
L.) is one of the most imperative staple food crops, with an annual production of 765 million tons globally to feed ∼40% world population. Genetic diversity in available germplasm is ...crucial for sustainable wheat improvement to ensure global food security. A diversity panel of 184 Pakistani wheat accessions was genotyped using 123,596 high-quality single nucleotide polymorphism (SNP) markers generated by genotyping-by-sequencing with 42% of the SNPs mapped on B, 36% on A, and 22% on D sub-genomes of wheat. Chromosome 2B contains the most SNPs (9,126), whereas 4D has the least (2,660) markers. The mean polymorphic information content, genetic diversity, and major allele frequency of the population were 0.157, 0.1844, and 0.87, respectively. Analysis of molecular variance revealed a higher genetic diversity (80%) within the sub-population than among the sub-populations (20%). The genome-wide linkage disequilibrium was 0.34 Mbp for the whole wheat genome. Among the three subgenomes, A has the highest LD decay value (0.29 Mbp), followed by B (0.2 Mbp) and D (0.07 Mbp) genomes, respectively. The results of population structure, principal coordinate analysis, phylogenetic tree, and kinship analysis also divided the whole population into three clusters comprising 31, 33, and 120 accessions in group 1, group 2, and group 3, respectively. All groups were dominated by the local wheat accessions. Estimation of genetic diversity will be a baseline for the selection of breeding parents for mutations and the genome-wide association and marker-assisted selection studies.
Skim exome capture genotyping in wheat Wang, Hongliang; Bernardo, Amy; St. Amand, Paul ...
The plant genome,
December 2023, 2023-Dec, 2023-12-00, 20231201, 2023-12-01, Letnik:
16, Številka:
4
Journal Article
Recenzirano
Odprti dostop
Next‐generation sequencing (NGS) technology advancements continue to reduce the cost of high‐throughput genome‐wide genotyping for breeding and genetics research. Skim sequencing, which surveys the ...entire genome at low coverage, has become feasible for quantitative trait locus (QTL) mapping and genomic selection in various crops. However, the genome complexity of allopolyploid crops such as wheat (Triticum aestivum L.) still poses a significant challenge for genome‐wide genotyping. Targeted sequencing of the protein‐coding regions (i.e., exome) reduces sequencing costs compared to whole genome re‐sequencing and can be used for marker discovery and genotyping. We developed a method called skim exome capture (SEC) that combines the strengths of these existing technologies and produces targeted genotyping data while decreasing the cost on a per‐sample basis compared to traditional exome capture. Specifically, we fragmented genomic DNA using a tagmentation approach, then enriched those fragments for the low‐copy genic portion of the genome using commercial wheat exome baits and multiplexed the sequencing at different levels to achieve desired coverage. We demonstrated that for a library of 48 samples, ∼7–8× target coverage was sufficient for high‐quality variant detection. For higher multiplexing levels of 528 and 1056 samples per library, we achieved an average coverage of 0.76× and 0.32×, respectively. Combining these lower coverage SEC sequencing data with genotype imputation using a customized wheat practical haplotype graph database that we developed, we identified hundreds of thousands of high‐quality genic variants across the genome. The SEC method can be used for high‐resolution QTL mapping, genome‐wide association studies, genomic selection, and other downstream applications.
Core Ideas
Combining strengths of existing sequencing platforms provides cost‐reducing savings per sample.
Targeted multiplexed wheat exome capture provides an alternative to reduced‐representation sequencing.
Informed imputation using customized wheat practical haplotype graph database identifies high‐quality variants across the wheat exome.
Fusarium head blight (FHB) is one of the prevalent fungal diseases of wheat worldwide. Exploring new FHB resistance quantitative trait loci (QTL) in adapted wheat cultivars is a critical step for ...breeding new FHB-resistant cultivars. In this study, we developed a population of 236 F5:7 recombinant inbred lines (RILs) using two popular Chinese wheat cultivars, Yangmai 158 and Zhengmai 9023, with moderate FHB resistance to identify the QTL for FHB type II resistance. This population was evaluated for percentage of symptomatic spikelets per spike (PSS) using single floret injection in repeated greenhouse experiments. Mean PSSs were 33.2% for Yangmai 158 and 30.3% for Zhengmai 9023. A genetic linkage map of 1002 single nucleotide polymorphisms (SNPs) generated by genotyping-by-sequencing (GBS) was constructed for the RIL population. Six QTL were identified for FHB resistance, and three of them were repeatable in the both experiments. Zhengmai 9023 contributed the resistance allele at one repeatable QTL, designated as Qfhb.7D, whereas Yangmai 158 contributed the resistance alleles at the other two repeatable QTL, Qfhb.3AL and Qfhb.2DS. The additional QTL, Qfhb.4AS was significant in the mean PSS, and Qfhb.2DL and Qfhb.7AS were significant in only one experiment. Replacement of each allele individually at the three repeatable QTL significantly changed PSSs. Qfhb.3AL, Qfhb.2DS, and Qfhb.7D explained 8.35% to 9.89%, 5.13% to 7.43%, and 6.15% to 9.32% of the phenotypic variations, respectively. The three repeatable QTL contributed by the two parents were additive and stacking the resistance alleles from all the three repeatable QTL showed the highest level of resistance in the current RIL population. Ten SNPs in the QTL regions of Qfhb.3AL, Qfhb.2DS, and Qfhb.7D were converted into KBioscience competitive allele-specific PCR (KASP) assays. One KASP marker for Qfhb.3AL was validated in a panel of wheat cultivars from China. Some of these KASP markers could be useful for marker-assisted selection to stack these QTL.
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