KASP markers to detect sub-chromosomal arm translocations between 6VS of Haynaldia villosa and 6AS of wheat

Abstract Key message A previously identified soybean maturity locus, E6, is discovered to be J, with the long juvenile allele in Paranagoiana now deemed j−x. Abstract Soybean grown at latitudes of ~20° or lower can produce lower grain yields due to the short days. This limitation can be overcome by using the long juvenile trait (LJ) which delays flowering under short day conditions. Two LJ loci have been mapped to the same location on Gm04, J and E6. The objective of this research was to investigate the e6 allele in ‘Paranagoiana’ and determine if E6 and J are the same locus or linked loci. KASP markers showed that e6 lines did not have the j−1 allele of LJ PI 159925. A population fixed for E1 but segregating for E6, with e6 introgressed from Paranagoiana, showed single gene control for flowering and maturity under short days. Sequencing Glyma.04G050200, the J gene, with long amplification Taq found that the e6 line ‘Paranagoiana’ contains a Ty1-copia retrotransposon of ~10,000 bp, inserted within exon 4. PCR amplification of the cDNA of Glyma.04G050200 also showed differences between the mRNA sequences (presence of insertion in j−x). Hence, we conclude that the loci E6 and J are one locus and deem this new variation found in Paranagoiana as j−x.

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Induction of 4VS chromosome recombinants using the CS ph1b mutant and mapping of the wheat yellow mosaic virus resistance gene from Haynaldia villosa

Theoretical and Applied Genetics ◽

10.1007/s00122-013-2181-y ◽

2013 ◽

Vol 126 (12) ◽

pp. 2921-2930 ◽

Cited By ~ 30

Author(s):

Renhui Zhao ◽

Haiyan Wang ◽

Jin Xiao ◽

Tongde Bie ◽

Shunhe Cheng ◽

...

Keyword(s):

Mosaic Virus ◽

Resistance Gene ◽

Virus Resistance ◽

Yellow Mosaic Virus ◽

Wheat Yellow Mosaic Virus ◽

Haynaldia Villosa ◽

Virus Resistance Gene

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RIESENPOLLENKÖRNER BEI DEN F1-BASTARDEN AEGILOPS SQUARROSA×HAYNALDIA VILLOSA UND AEGILOPS CAUDATA×AEGILOPS SPELTOIDES

The Japanese Journal of Genetics ◽

10.1266/jjg.12.239 ◽

1936 ◽

Vol 12 (5) ◽

pp. 239-256 ◽

Cited By ~ 3

Author(s):

H. KIHARA ◽

F. LILIENFELD

Keyword(s):

Aegilops Speltoides ◽

Haynaldia Villosa ◽

Aegilops Squarrosa ◽

Aegilops Caudata

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Association of KASP markers with Hessian fly resistance in wheat of diverse origin

Euphytica ◽

10.1007/s10681-018-2228-x ◽

2018 ◽

Vol 214 (8) ◽

Author(s):

Damian Collins ◽

Livinus Emebiri ◽

Mui-Keng Tan ◽

Mustapha El Bouhssini ◽

Ossie Wildman

Keyword(s):

Hessian Fly ◽

Hessian Fly Resistance ◽

Diverse Origin ◽

Kasp Markers

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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

Phytopathology ◽

10.1094/phyto-04-17-0153-r ◽

2018 ◽

Vol 108 (1) ◽

pp. 103-113 ◽

Cited By ~ 13

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.

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Development of KASP Markers for Germplasm Characterization and Fingerprinting Identification of Broccoli in China

10.21203/rs.3.rs-60988/v1 ◽

2020 ◽

Author(s):

Yusen Shen ◽

Jiansheng Wang ◽

Huifang Yu ◽

Xiaoguang Sheng ◽

Zhenqing Zhao ◽

...

Keyword(s):

Genetic Diversity ◽

Marker Assisted Selection ◽

Genetic Relationships ◽

Cost Effective ◽

Germplasm Characterization ◽

2D Barcode ◽

New Type ◽

Generation Sequencing ◽

Kasp Markers ◽

Selection Of

Abstract Background: Broccoli (Brassica oleracea var. italica) is a vegetable widely cultivated in China. Many new-type broccoli cultivars were bred and developed by Chinese breeders during the recent three decades. However, the broccoli cultivar nomenclature and detailed information of genetic relationships among broccoli germplasms are unclear. Results: The present study identified millions of SNPs by next-generation sequencing of 23 representative broccoli lines. Through several steps of selection, 100 SNPs were successfully converted into KASP markers, and used to evaluate the genetic diversity, genetic relationship, and population structure of 392 broccoli accessions, which represent the mainly broccoli breeding materials in China. The initial, introduced and improved accessions were well clustered, though some accessions were overlapped between groups, probably reflecting the fact that breeding activities led to genetic similarities. To make the KASP genotyping more efficient and cost-effective, 25 of the 100 KASPs were selected for fingerprinting of all accessions, and the 2D barcode contained fingerprinting information were generated for elite varieties. Conclusion: The KASP markers developed in this study provided an efficient way for germplasm characterization, DNA fingerprinting, seed purity identification, and marker-assisted selection of broccoli in China.

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Fine Mapping of qd1, a Dominant Gene that Regulates Stem Elongation in Bread Wheat

Frontiers in Genetics ◽

10.3389/fgene.2021.793572 ◽

2021 ◽

Vol 12 ◽

Author(s):

Yongdun Xie ◽

Weiwei Zeng ◽

Chaojie Wang ◽

Daxing Xu ◽

Huijun Guo ◽

...

Keyword(s):

Bread Wheat ◽

Stem Elongation ◽

Dominant Gene ◽

Nucleotide Polymorphisms ◽

Sequencing Data ◽

Specific Pcr ◽

Yield Determination ◽

Allele Specific ◽

Stem Development ◽

Kasp Markers

Stem elongation is a critical phase for yield determination and, as a major trait, is targeted for manipulation for improvement in bread wheat (Triticum aestivum L.). In a previous study, we characterized a mutant showing rapid stem elongation but with no effect on plant height at maturity. The present study aimed to finely map the underlying mutated gene, qd1, in this mutant. By analyzing an F2 segregating population consisting of 606 individuals, we found that the qd1 gene behaved in a dominant manner. Moreover, by using the bulked segregant RNA sequencing (BSR-seq)-based linkage analysis method, we initially mapped the qd1 gene to a 13.55 Mb region on chromosome 4B (from 15.41 to 28.96 Mb). This result was further confirmed in F2 and BC3F2 segregating populations. Furthermore, by using transcriptome sequencing data, we developed 14 Kompetitive Allele-Specific PCR (KASP) markers and then mapped the qd1 gene to a smaller and more precise 5.08 Mb interval from 26.80 to 31.88 Mb. To develop additional markers to finely map the qd1 gene, a total of 4,481 single-nucleotide polymorphisms (SNPs) within the 5.08 Mb interval were screened, and 25 KASP markers were developed based on 10x-depth genome resequencing data from both wild-type (WT) and mutant plants. The qd1 gene was finally mapped to a 1.33 Mb interval from 28.86 to 30.19 Mb on chromosome 4B. Four candidate genes were identified in this region. Among them, the expression pattern of only TraesCS4B02G042300 in the stems was concurrent with the stem development of the mutant and WT. The qd1 gene could be used in conjunction with molecular markers to manipulate stem development in the future.

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Detection of a Major QTL and Development of KASP Markers for Seed Weight by Combining QTL-seq, QTL-mapping and RNA-seq in Peanut

10.21203/rs.3.rs-531536/v1 ◽

2021 ◽

Author(s):

Zhihui Wang ◽

Liying Yan ◽

Yuning Chen ◽

Xin Wang ◽

Dongxin Huai ◽

...

Keyword(s):

Qtl Mapping ◽

Candidate Genes ◽

Seed Development ◽

Seed Weight ◽

Molecular Mechanisms ◽

Large Contribution ◽

Phenotypic Variance ◽

Rna Seq ◽

Late Stages ◽

Kasp Markers

Abstract Seed weight is a major target of peanut breeding as an important component of seed yield. However, relatively little is known about QTLs and candidate genes associated with seed weight in peanut. In this study, three major QTLs on chromosomes A05, B02 and B06 were determined by applying NGS-based QTL-seq approach for a RIL population. These three QTL regions have been successfully narrowed down through newly developed SNP and SSR markers based on traditional QTL mapping. Among these three QTL regions, qSWB06.3 exhibited stable expression with large contribution to phenotypic variance across all environments. Furthermore, RNA-seq were applied for early, middle and late stages of seed development, and differentially expression genes (DEGs) were identified in ubiquitin-proteasome pathway, serine/threonine protein pathway and signal transduction of hormones and transcription factors. Notably, DEGs at early stage were majorly related to regulating cell division, whereas DEGs at middle and late stages were mainly associated with cell expansion during seed development. Through integrating SNP variation, gene expression and functional annotation, candidate genes related to seed weight in qSWB06.3 were predicted and distinct expression pattern of those genes were exhibited using qRT-PCR. In addition, KASP-markers in qSWB06.3 were successfully validated in diverse peanut varieties and the alleles of parent Zhonghua16 in qSWB06.3 was associated with high seed weight. This suggested that qSWB06.3 was reliable and the markers in qSWB06.3 could be deployed in marker-assisted breeding to enhance seed weight. This study provided insights into the understanding of genetic and molecular mechanisms of seed weight in peanut.

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