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1.
Sci Rep ; 10(1): 10908, 2020 Jul 02.
Artigo em Inglês | MEDLINE | ID: mdl-32616836

RESUMO

Stripe or yellow rust (YR) caused by Puccinia striiformis Westend. f. sp. tritici Erikss. is a persistent biotic-stress threatening global wheat production. To broaden our understanding of the shared genetic basis of YR resistance across multi-site and multi-year evaluations, we performed a large genome-wide association study using 43,706 YR observations on 23,346 wheat lines from the International Maize and Wheat Improvement Center evaluated between 2013 and 2019 at sites in India, Kenya and Mexico, against predominant races prevalent in the countries. We identified 114 repeatable markers tagging 20 quantitative trait loci (QTL) associated with YR on ten chromosomes including 1D, 2A, 2B, 2D, 3A, 4A, 4D, 5A, 5B and 6B, among which four QTL, QYr.cim-2DL.2, QYr.cim-2AS.1, QYr.cim-2BS.2 and QYr.cim-2BS.3 were significant in more than ten datasets. Furthermore, we report YR-associated allelic fingerprints for the largest panel of wheat breeding lines (52,067 lines) till date, creating substantial opportunities for YR favorable allele enrichment using molecular markers. Overall, the markers and fingerprints reported in this study provide excellent insights into the genetic architecture of YR resistance in different geographical regions, time-periods and wheat germplasm and are a huge resource to the global wheat breeding community for accelerating YR resistance breeding efforts.

2.
Int J Mol Sci ; 20(21)2019 Oct 31.
Artigo em Inglês | MEDLINE | ID: mdl-31683619

RESUMO

Tan spot (TS) and Septoria nodorum blotch (SNB) induced by Pyrenophora tritici-repentis and Parastagonospora nodorum, respectively, cause significant yield losses and adversely affect grain quality. The objectives of this study were to decipher the genetics and map the resistance to TS and SNB in the PBW343/Kenya Nyangumi (KN) population comprising 204 F6 recombinant inbred lines (RILs). Disease screening was performed at the seedling stage under greenhouse conditions. TS was induced by P. tritici-repentis isolate MexPtr1 while SNB by P. nodorum isolate MexSN1. Segregation pattern of the RILs indicated that resistance to TS and SNB in this population was quantitative. Diversity Array Technology (DArTs) and simple sequence repeats (SSRs) markers were used to identify the quantitative trait loci (QTL) for the diseases using inclusive composite interval mapping (ICIM). Seven significant additive QTLs for TS resistance explaining 2.98 to 23.32% of the phenotypic variation were identified on chromosomes 1A, 1B, 5B, 7B and 7D. For SNB, five QTLs were found on chromosomes 1A, 5A, and 5B, explaining 5.24 to 20.87% of the phenotypic variation. The TS QTL on 1B chromosome coincided with the pleiotropic adult plant resistance (APR) gene Lr46/Yr29/Pm39. This is the first report of the APR gene Lr46/Yr29/Pm39 contributing to TS resistance.


Assuntos
Resistência à Doença/genética , Genes de Plantas/genética , Doenças das Plantas/genética , Locos de Características Quantitativas/genética , Plântula/genética , Triticum/genética , Ascomicetos/fisiologia , Mapeamento Cromossômico , Cromossomos de Plantas/genética , Genótipo , Endogamia , Quênia , Repetições de Microssatélites , Fenótipo , Doenças das Plantas/microbiologia , Recombinação Genética , Plântula/microbiologia , Triticum/microbiologia
3.
Nat Genet ; 51(10): 1530-1539, 2019 10.
Artigo em Inglês | MEDLINE | ID: mdl-31548720

RESUMO

Bread wheat improvement using genomic tools is essential for accelerating trait genetic gains. Here we report the genomic predictabilities of 35 key traits and demonstrate the potential of genomic selection for wheat end-use quality. We also performed a large genome-wide association study that identified several significant marker-trait associations for 50 traits evaluated in South Asia, Africa and the Americas. Furthermore, we built a reference wheat genotype-phenotype map, explored allele frequency dynamics over time and fingerprinted 44,624 wheat lines for trait-associated markers, generating over 7.6 million data points, which together will provide a valuable resource to the wheat community for enhancing productivity and stress resilience.


Assuntos
Resistência à Doença/genética , Genômica/métodos , Locos de Características Quantitativas , Estresse Fisiológico/imunologia , Triticum/crescimento & desenvolvimento , Triticum/imunologia , Ascomicetos/fisiologia , Mapeamento Cromossômico , Grão Comestível/genética , Grão Comestível/crescimento & desenvolvimento , Estudos de Associação Genética , Marcadores Genéticos , Genoma de Planta , Estudo de Associação Genômica Ampla , Melhoramento Vegetal , Doenças das Plantas/genética , Doenças das Plantas/microbiologia , Seleção Genética , Estresse Fisiológico/genética , Triticum/genética
4.
Sci Rep ; 9(1): 12355, 2019 08 26.
Artigo em Inglês | MEDLINE | ID: mdl-31451719

RESUMO

Synthetic hexaploid (SH) wheat (AABBD'D') is developed by artificially generating a fertile hybrid between tetraploid durum wheat (Triticum turgidum, AABB) and diploid wild goat grass (Aegilops tauschii, D'D'). Over three decades, the International Maize and Wheat Improvement Center (CIMMYT) has developed and utilized SH wheat to bridge gene transfer from Ae. tauschii and durum wheat to hexaploid bread wheat. This is a unique example of success utilizing wild relatives in mainstream breeding at large scale worldwide. Our study aimed to determine the genetic contribution of SH wheat to CIMMYT's global spring bread wheat breeding program. We estimated the theoretical and empirical contribution of D' to synthetic derivative lines using the ancestral pedigree and marker information using over 1,600 advanced lines and their parents. The average marker-estimated D' contribution was 17.5% with difference in genome segments suggesting application of differential selection pressure. The pedigree-based contribution was correlated with marker-based estimates without providing chromosome segment specific variation. Results from international yield trials showed that 20% of the lines were synthetic derived with an average D' contribution of 15.6%. Our results underline the importance of SH wheat in maintaining and enhancing genetic diversity and genetic gain over years and is important for development of a more targeted introgression strategy. The study provides retrospective view into development and utilization of SH in the CIMMYT Global Wheat Program.

5.
Int J Mol Sci ; 19(12)2018 Dec 14.
Artigo em Inglês | MEDLINE | ID: mdl-30558200

RESUMO

Spot blotch (SB) is an important fungal disease of wheat in South Asia and South America. Host resistance is regarded as an economical and environmentally friendly approach of controlling SB, and the inheritance of resistance is mostly quantitative. In order to gain a better understanding on the SB resistance mechanism in CIMMYT germplasm, two bi-parental mapping populations were generated, both comprising 232 F2:7 progenies. Elite CIMMYT breeding lines, BARTAI and WUYA, were used as resistant parents, whereas CIANO T79 was used as susceptible parent in both populations. The two populations were evaluated for field SB resistance at CIMMYT's Agua Fria station for three consecutive years, from the 2012⁻2013 to 2014⁻2015 cropping seasons. Phenological traits like plant height (PH) and days to heading (DH) were also determined. Genotyping was performed using the DArTSeq genotyping-by-sequencing (GBS) platform, and a few D-genome specific SNPs and those for phenological traits were integrated for analysis. The most prominent quantitative trait locus (QTL) in both populations was found on chromosome 5AL at the Vrn-A1 locus, explaining phenotypic variations of 7⁻27%. Minor QTL were found on chromosomes 1B, 3A, 3B, 4B, 4D, 5B and 6D in BARTAI and on chromosomes 1B, 2A, 2D and 4B in WUYA, whereas minor QTL contributed by CIANO T79 were identified on chromosome 1B, 1D, 3A, 4B and 7A. In summary, resistance to SB in the two mapping populations was controlled by multiple minor QTL, with strong influence from Vrn-A1.


Assuntos
Mapeamento Cromossômico/métodos , Resistência à Doença , Locos de Características Quantitativas , Triticum/genética , Cromossomos de Plantas/genética , Genótipo , Fenótipo , Melhoramento Vegetal , Doenças das Plantas/microbiologia , Sementes/genética , Triticum/anatomia & histologia , Triticum/crescimento & desenvolvimento
6.
Sci Rep ; 8(1): 13526, 2018 09 10.
Artigo em Inglês | MEDLINE | ID: mdl-30201978

RESUMO

Wheat is an important staple that acts as a primary source of dietary energy, protein, and essential micronutrients such as iron (Fe) and zinc (Zn) for the world's population. Approximately two billion people suffer from micronutrient deficiency, thus breeders have crossed high Zn progenitors such as synthetic hexaploid wheat, T. dicoccum, T. spelta, and landraces to generate wheat varieties with competitive yield and enhanced grain Zn that are being adopted by farmers in South Asia. Here we report a genome-wide association study (GWAS) using the wheat Illumina iSelect 90 K Infinitum SNP array to characterize grain Zn concentrations in 330 bread wheat lines. Grain Zn phenotype of this HarvestPlus Association Mapping (HPAM) panel was evaluated across a range of environments in India and Mexico. GWAS analysis revealed 39 marker-trait associations for grain Zn. Two larger effect QTL regions were found on chromosomes 2 and 7. Candidate genes (among them zinc finger motif of transcription-factors and metal-ion binding genes) were associated with the QTL. The linked markers and associated candidate genes identified in this study are being validated in new biparental mapping populations for marker-assisted breeding.


Assuntos
Biofortificação , Grão Comestível/genética , Locos de Características Quantitativas , Triticum/genética , Zinco/análise , Mapeamento Cromossômico , Cromossomos de Plantas/genética , Grão Comestível/química , Genoma de Planta/genética , Estudo de Associação Genômica Ampla , Índia , México , Melhoramento Vegetal/métodos , Proteínas de Plantas/genética , Plantas Geneticamente Modificadas/química , Plantas Geneticamente Modificadas/genética , Polimorfismo de Nucleotídeo Único , Sementes/química , Sementes/genética , Triticum/química , Dedos de Zinco/genética
7.
Plant Methods ; 12: 35, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-27347001

RESUMO

BACKGROUND: Low cost unmanned aerial systems (UAS) have great potential for rapid proximal measurements of plants in agriculture. In the context of plant breeding and genetics, current approaches for phenotyping a large number of breeding lines under field conditions require substantial investments in time, cost, and labor. For field-based high-throughput phenotyping (HTP), UAS platforms can provide high-resolution measurements for small plot research, while enabling the rapid assessment of tens-of-thousands of field plots. The objective of this study was to complete a baseline assessment of the utility of UAS in assessment field trials as commonly implemented in wheat breeding programs. We developed a semi-automated image-processing pipeline to extract plot level data from UAS imagery. The image dataset was processed using a photogrammetric pipeline based on image orientation and radiometric calibration to produce orthomosaic images. We also examined the relationships between vegetation indices (VIs) extracted from high spatial resolution multispectral imagery collected with two different UAS systems (eBee Ag carrying MultiSpec 4C camera, and IRIS+ quadcopter carrying modified NIR Canon S100) and ground truth spectral data from hand-held spectroradiometer. RESULTS: We found good correlation between the VIs obtained from UAS platforms and ground-truth measurements and observed high broad-sense heritability for VIs. We determined radiometric calibration methods developed for satellite imagery significantly improved the precision of VIs from the UAS. We observed VIs extracted from calibrated images of Canon S100 had a significantly higher correlation to the spectroradiometer (r = 0.76) than VIs from the MultiSpec 4C camera (r = 0.64). Their correlation to spectroradiometer readings was as high as or higher than repeated measurements with the spectroradiometer per se. CONCLUSION: The approaches described here for UAS imaging and extraction of proximal sensing data enable collection of HTP measurements on the scale and with the precision needed for powerful selection tools in plant breeding. Low-cost UAS platforms have great potential for use as a selection tool in plant breeding programs. In the scope of tools development, the pipeline developed in this study can be effectively employed for other UAS and also other crops planted in breeding nurseries.

8.
BMC Genomics ; 16: 216, 2015 Mar 19.
Artigo em Inglês | MEDLINE | ID: mdl-25887001

RESUMO

BACKGROUND: Genotyping-by-sequencing (GBS) is a high-throughput genotyping approach that is starting to be used in several crop species, including bread wheat. Anchoring GBS tags on chromosomes is an important step towards utilizing them for wheat genetic improvement. Here we use genetic linkage mapping to construct a consensus map containing 28644 GBS markers. RESULTS: Three RIL populations, PBW343 × Kingbird, PBW343 × Kenya Swara and PBW343 × Muu, which share a common parent, were used to minimize the impact of potential structural genomic variation on consensus-map quality. The consensus map comprised 3757 unique positions, and the average marker distance was 0.88 cM, obtained by calculating the average distance between two adjacent unique positions. Significant variation of segregation distortion was observed across the three populations. The consensus map was validated by comparing positions of known rust resistance genes, and comparing them to wheat reference genome sequences recently published by the International Wheat Genome Sequencing Consortium, Rye and Ae. tauschii genomes. Three well-characterized rust resistance genes (Sr58/Lr46/Yr29, Sr2/Yr30/Lr27, and Sr57/Lr34/Yr18) and 15 published QTLs for wheat rusts were validated with high resolution. Fifty-two per cent of GBS tags on the consensus map were successfully aligned through BLAST to the right chromosomes on the wheat reference genome sequence. CONCLUSION: The consensus map should provide a useful basis for analyzing genome-wide variation of complex traits. The identified genes can then be explored as genetic markers to be used in genomic applications in wheat breeding.


Assuntos
Mapeamento Cromossômico , Resistência à Doença/genética , Sequenciamento de Nucleotídeos em Larga Escala , Característica Quantitativa Herdável , Triticum/genética , Cromossomos de Plantas , Evolução Molecular , Ligação Genética , Marcadores Genéticos , Genoma de Planta , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Endogamia , Doenças das Plantas/genética , Locos de Características Quantitativas
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