Centenary of Soil and Air Borne Wheat Karnal Bunt Disease Research: A Review

Karnal bunt (KB) of wheat (Triticum aestivum L.), known as partial bunt has its origin in Karnal, India and is caused by Tilletia indica (Ti). Its incidence had grown drastically since late 1960s from northwestern India to northern India in early 1970s. It is a seed, air and soil borne pathogen mainly affecting common wheat, durum wheat, triticale and other related species. The seeds become inedible, inviable and infertile with the precedence of trimethylamine secreted by teliospores in the infected seeds. Initially the causal pathogen was named Tilletia indica but was later renamed Neovossia indica. The black powdered smelly spores remain viable for years in soil, wheat straw and farmyard manure as primary sources of inoculum. The losses reported were as high as 40% in India and also the cumulative reduction of national farm income in USA was USD 5.3 billion due to KB. The present review utilizes information from literature of the past 100 years, since 1909, to provide a comprehensive and updated understanding of KB, its causal pathogen, biology, epidemiology, pathogenesis, etc. Next generation sequencing (NGS) is gaining popularity in revolutionizing KB genomics for understanding and improving agronomic traits like yield, disease tolerance and disease resistance. Genetic resistance is the best way to manage KB, which may be achieved through detection of genes/quantitative trait loci (QTLs). The genome-wide association studies can be applied to reveal the association mapping panel for understanding and obtaining the KB resistance locus on the wheat genome, which can be crossed with elite wheat cultivars globally for a diverse wheat breeding program. The review discusses the current NGS-based genomic studies, assembly, annotations, resistant QTLs, GWAS, technology landscape of diagnostics and management of KB. The compiled exhaustive information can be beneficial to the wheat breeders for better understanding of incidence of disease in endeavor of quality production of the crop.

Download Full-text

Genome-wide association studies of 14 agronomic traits in rice landraces

Nature Genetics ◽

10.1038/ng.695 ◽

2010 ◽

Vol 42 (11) ◽

pp. 961-967 ◽

Cited By ~ 1156

Author(s):

Xuehui Huang ◽

Xinghua Wei ◽

Tao Sang ◽

Qiang Zhao ◽

Qi Feng ◽

...

Keyword(s):

Agronomic Traits ◽

Association Studies ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Rice Landraces ◽

Genome Wide

Download Full-text

Meta-Analysis Reveals Consensus Genomic Regions Associated with Multiple Disease Resistance in Wheat ( Triticum Aestivum L.)

10.21203/rs.3.rs-773587/v1 ◽

2021 ◽

Author(s):

Dinesh Kumar Saini ◽

Amneek Chahal ◽

Neeraj Pal ◽

Puja Srivast ◽

Pushpendra Kumar Gupta

Keyword(s):

Disease Resistance ◽

Physical Map ◽

Association Studies ◽

Meta Analysis ◽

Septoria Tritici Blotch ◽

Septoria Tritici ◽

Karnal Bunt ◽

Genome Wide Association Studies ◽

Head Blight ◽

Multiple Disease Resistance

Abstract In wheat, meta-QTLs (MQTLs), and candidate genes (CGs) were identified for multiple disease resistance (MDR). For this purpose, information was collected from 58 studies for mapping QTLs for resistance to one or more of the five diseases. As many as 493 QTLs were available from these studies, which were distributed in five diseases as follows: septoria tritici blotch (STB) 126 QTLs; septoria nodorum blotch (SNB), 103; fusarium head blight (FHB), 184; karnal bunt (KB), 66, and loose smut (LS), 14. Of these 493 QTLs, only 291 QTLs could be projected onto a consensus genetic map, giving 63 MQTLs. The CI of the MQTLs ranged from 0.04 to 15.31 cM with an average of 3.09 cM per MQTL. This is a ~ 4.39 fold reduction from the CI of initial QTLs, which ranged from 0 to 197.6 cM, with a mean of 13.57 cM. Of 63 MQTLs, 60 were anchored to the reference physical map of wheat (the physical interval of these MQTLs ranged from 0.30 to 726.01 Mb with an average of 74.09 Mb). Thirty-eight (38) of these MQTLs were verified using marker-trait associations (MTAs) derived from genome-wide association studies. As many as 874 CGs were also identified which were further investigated for differential expression using data from five transcriptome studies, resulting in 194 differentially expressed genes (DEGs). Among the DEGs, 85 genes had functions previously reported to be associated with disease resistance. These results should prove useful for fine mapping of MDR genes and marker-assisted breeding.

Download Full-text

Genome-wide association study of agronomic traits in bread wheat reveals novel putative alleles for future breeding programs

BMC Plant Biology ◽

10.1186/s12870-019-2165-4 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 11

Author(s):

Yousef Rahimi ◽

Mohammad Reza Bihamta ◽

Alireza Taleei ◽

Hadi Alipour ◽

Pär K. Ingvarsson

Keyword(s):

Bread Wheat ◽

Genome Wide Association Study ◽

Agronomic Traits ◽

Association Studies ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Wheat Varieties ◽

Data Set ◽

Protein Coding ◽

Genome Wide

Abstract Background Identification of loci for agronomic traits and characterization of their genetic architecture are crucial in marker-assisted selection (MAS). Genome-wide association studies (GWAS) have increasingly been used as potent tools in identifying marker-trait associations (MTAs). The introduction of new adaptive alleles in the diverse genetic backgrounds may help to improve grain yield of old or newly developed varieties of wheat to balance supply and demand throughout the world. Landraces collected from different climate zones can be an invaluable resource for such adaptive alleles. Results GWAS was performed using a collection of 298 Iranian bread wheat varieties and landraces to explore the genetic basis of agronomic traits during 2016–2018 cropping seasons under normal (well-watered) and stressed (rain-fed) conditions. A high-quality genotyping by sequencing (GBS) dataset was obtained using either all original single nucleotide polymorphism (SNP, 10938 SNPs) or with additional imputation (46,862 SNPs) based on W7984 reference genome. The results confirm that the B genome carries the highest number of significant marker pairs in both varieties (49,880, 27.37%) and landraces (55,086, 28.99%). The strongest linkage disequilibrium (LD) between pairs of markers was observed on chromosome 2D (0.296). LD decay was lower in the D genome, compared to the A and B genomes. Association mapping under two tested environments yielded a total of 313 and 394 significant (−log10P >3) MTAs for the original and imputed SNP data sets, respectively. Gene ontology results showed that 27 and 27.5% of MTAs of SNPs in the original set were located in protein-coding regions for well-watered and rain-fed conditions, respectively. While, for the imputed data set 22.6 and 16.6% of MTAs represented in protein-coding genes for the well-watered and rain-fed conditions, respectively. Conclusions Our finding suggests that Iranian bread wheat landraces harbor valuable alleles that are adaptive under drought stress conditions. MTAs located within coding genes can be utilized in genome-based breeding of new wheat varieties. Although imputation of missing data increased the number of MTAs, the fraction of these MTAs located in coding genes were decreased across the different sub-genomes.

Download Full-text

Genomic Prediction and Genome-Wide Association Studies of Flour Yield and Alveograph Quality Traits Using Advanced Winter Wheat Breeding Material

Genes ◽

10.3390/genes10090669 ◽

2019 ◽

Vol 10 (9) ◽

pp. 669 ◽

Cited By ~ 2

Author(s):

Peter S. Kristensen ◽

Just Jensen ◽

Jeppe R. Andersen ◽

Carlos Guzmán ◽

Jihad Orabi ◽

...

Keyword(s):

Winter Wheat ◽

Genomic Prediction ◽

Association Studies ◽

Wheat Breeding ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Quality Traits ◽

Breeding Programs ◽

Genome Wide ◽

Flour Yield

Use of genetic markers and genomic prediction might improve genetic gain for quality traits in wheat breeding programs. Here, flour yield and Alveograph quality traits were inspected in 635 F6 winter wheat breeding lines from two breeding cycles. Genome-wide association studies revealed single nucleotide polymorphisms (SNPs) on chromosome 5D significantly associated with flour yield, Alveograph P (dough tenacity), and Alveograph W (dough strength). Additionally, SNPs on chromosome 1D were associated with Alveograph P and W, SNPs on chromosome 1B were associated with Alveograph P, and SNPs on chromosome 4A were associated with Alveograph L (dough extensibility). Predictive abilities based on genomic best linear unbiased prediction (GBLUP) models ranged from 0.50 for flour yield to 0.79 for Alveograph W based on a leave-one-out cross-validation strategy. Predictive abilities were negatively affected by smaller training set sizes, lower genetic relationship between lines in training and validation sets, and by genotype–environment (G×E) interactions. Bayesian Power Lasso models and genomic feature models resulted in similar or slightly improved predictions compared to GBLUP models. SNPs with the largest effects can be used for screening large numbers of lines in early generations in breeding programs to select lines that potentially have good quality traits. In later generations, genomic predictions might be used for a more accurate selection of high quality wheat lines.

Download Full-text

Assembly of chromosome-scale and allele-aware autotetraploid genome of the Chinese alfalfa cultivar Zhongmu-4 and identification of SNP loci associated with 27 agronomic traits

10.1101/2021.02.21.428692 ◽

2021 ◽

Cited By ~ 1

Author(s):

Ruicai Long ◽

Fan Zhang ◽

Zhiwu Zhang ◽

Mingna Li ◽

Lin Chen ◽

...

Keyword(s):

Genome Sequence ◽

Single Molecule ◽

Agronomic Traits ◽

Association Studies ◽

Genetic Research ◽

Chromosome 1 ◽

Genome Wide Association Studies ◽

Forage Crops ◽

Legume Crop ◽

Population Structure Analysis

AbstractAlfalfa (Medicago sativaL.), the most valuable perennial legume crop, referred to as “Queen of the Forages” for its high nutritional value and yield production among forage crops. Comprehensive genomic information of germplasm resources from different ecological regions and modern breeding strategies, such as molecular-marker assisted breeding are of great importance to breed new alfalfa varieties with environmental resilience. Here, we report assembly of the genome sequence of Zhongmu-4 (ZM-4), one of the most planted cultivars in China, and identification of SNPs associated with alfalfa agronomic traits by Genome-wide Association Studies (GWAS). Sequence of 32 allelic chromosomes was assembled successfully by single molecule real time sequencing and Hi-C technique with ALLHiC algorithm. About 2.74 Gbp contigs, accounting for 88.39% of the estimated genome, were assembled with 2.56 Gbp contigs anchored to 32 pseudo-chromosomes. In comparison withM. truncatulaA17, distinctive inversion and translocation on chromosome 1, and between chromosome 4 and 8, respectively, were detected. Moreover, we conducted resequencing of 220 alfalfa accessions collected globally and performed GWAS analysis based on our assembled genome. Population structure analysis demonstrated that alfalfa has a complex genetic relationship among germplasm with different geographic origins. GWAS identified 101 SNPs associated with 27 out of 93 agronomic traits. The updated chromosome-scale and allele-aware genome sequence, coupled with the resequencing data of most global alfalfa germplasm, provides valuable information for alfalfa genetic research, and further analysis of major SNP loci will accelerate unravelling the molecular basis of important agronomic traits and facilitate genetic improvement of alfalfa.

Download Full-text

The impact of transposable elements on tomato diversity

10.1101/2020.06.04.133835 ◽

2020 ◽

Cited By ~ 2

Author(s):

Marisol Domínguez ◽

Elise Dugas ◽

Médine Benchouaia ◽

Basile Leduque ◽

José Jimenez-Gomez ◽

...

Keyword(s):

Transposable Elements ◽

Agronomic Traits ◽

Association Studies ◽

Low Frequency ◽

Genome Wide Association Studies ◽

Environmental Response ◽

Whole Genome Resequencing ◽

Wild Accessions ◽

Genetic Pool ◽

The Impact

ABSTRACTTomatoes come in a multitude of shapes and flavors despite a narrow genetic pool. Here, we leveraged whole-genome resequencing data available for 602 cultivated and wild accessions to determine the contribution of transposable elements (TEs) to tomato diversity. We identified 6,906 TE insertions polymorphisms (TIPs), which result from the mobilization of 337 distinct TE families. Most TIPs are low frequency variants and disproportionately located within or adjacent to genes involved in environmental response. In addition, we show that genic TE insertions tend to have strong transcriptional effects and can notably lead to the generation of multiple transcript isoforms. We also uncovered through genome-wide association studies (GWAS) ~180 TIPs associated with extreme variations in major agronomic traits or secondary metabolites. Importantly, these TIPs tend to affect loci that are distinct from those tagged by SNPs. Collectively, our findings suggest a unique and important role for TE mobilization in tomato diversification, with important implications for future breeding.

Download Full-text

Genome-wide Identification of Powdery Mildew Resistance in Common Bean

10.21203/rs.3.rs-27731/v2 ◽

2020 ◽

Author(s):

Papias Hongera Binagwa ◽

Sy M. Traore ◽

Marceline Egnin ◽

Gregory C. Bernard ◽

Inocent Ritte ◽

...

Keyword(s):

Disease Resistance ◽

Common Bean ◽

Resistance Genes ◽

Agronomic Traits ◽

Association Studies ◽

Significant Snps ◽

Genome Wide Association Studies ◽

Genome Wide ◽

Disease Resistance Protein ◽

Resistance Protein

Abstract Background: Genome-wide association studies (GWAS) was utilized to detect genetic variations related to the powdery mildew (PM) resistance and several agronomic traits in common bean. However, its application in common bean and the PM interactions to identify genes and their location in the common bean genome has not been fully addressed. Results: Genome-wide association studies (GWAS) through marker-trait association are useful molecular tools for the identification of disease resistance and other agronomic traits. SNP genotyping with a BeadChip containing 5398 SNPs was used to detect genetic variations related to resistance to PM disease in a panel of 206 genotypes grown under field conditions for two consecutive years. Significant SNPs identified on chromosomes 4 and 10 (Pv04 and Pv10) were repeatable, confirming the reliability of the phenotypic data scored from the genotypes grown in two locations within two years. A cluster of resistance genes was revealed on the chromosome 4 of common bean genome among which CNL and TNL like resistance genes were identified. Furthermore, two resistance genes Phavu_010G1320001g and Phavu_010G136800g were also identified on Pv10; further sequence analysis showed that these genes were homologs to the Arabidopsis disease resistance protein (RLM1A-like) and the putative disease resistance protein (At4g11170.1), respectively. Two LRR receptor-like kinases (RLK) were also identified on Pv11 in samples collected in 2018 only. Many genes encoding auxin-responsive protein, TIFY10A protein, growth-regulating factor 5-like, ubiquitin-like protein, cell wall protein RBR3-like protein related to PM resistance were identified nearby significant SNPs. These results suggested that the resistance to PM pathogen involves a network of many genes constitutively co-expressed and may generate several layers of defense barriers or inducible reactions.Conclusion: Our results provide new insights into common bean and PM interactions, and revealed putative resistance genes as well as their location on common bean genome that could be used for marker-assisted selection, functional genomic study approaches to confirm the role of these putative genes; hence, developing common bean resistance lines to the PM disease.

Download Full-text

Validation of Bread Wheat KASP Markers in Durum Wheat Lines in Kazakhstan

Proceedings of the Latvian Academy of Sciences. Section B. Natural, Exact, and Applied Sciences. ◽

10.2478/prolas-2019-0071 ◽

2019 ◽

Vol 73 (5) ◽

pp. 462-465

Author(s):

Shynar Anuarbek ◽

Saule Abugalieva ◽

Yerlan Turuspekov

Keyword(s):

Durum Wheat ◽

Bread Wheat ◽

Agronomic Traits ◽

Association Studies ◽

Yield Potential ◽

Genome Wide Association Studies ◽

Specific Pcr ◽

Allele Specific ◽

Wheat Lines ◽

Polyploid Crops

Abstract Development of efficient DNA markers plays an important role in modern breeding projects of many crops, including cultivated hexaploid bread wheat (BW) and tetraploid durum wheat (DW). Findings of genome-wide association studies on major polyploid crops, such as BW, may also help in molecular breeding studies in relative cultivated species with a similar genetic background, including DW. Therefore, the validation of identified quantitative trait loci or marker-trait associations is an important preliminary step in marker-assisted selection (MAS) oriented projects. In this study, thirty-two SNP (single nucleotide polymorphism) markers of six agronomic traits identified in BW, harvested in Kazakhstan, were converted to KASP (Kompetitive Allele-Specific PCR) as-says. Generated 32 KASP assays were used in the analysis of 29 DW accessions from Kazakhstan. Firstly, the group of DW accessions was tested using replicated and randomised one-metre blocks in field conditions of southeast Kazakhstan and evaluated for main agronomic traits. The analysis showed that 14 KASP assays were polymorphic in the scoring of 29 DW accessions. The t-test suggested that the segregation in eight KASP assays was significantly associated with five agronomic traits. The study confirms robustness of KASP assays in MAS of DW breeding projects for the improvement of yield potential.

Download Full-text

Genome-wide association studies of ionomic and agronomic traits in USDA mini core collection of rice and comparative analyses of different mapping methods

10.21203/rs.2.22202/v3 ◽

2020 ◽

Author(s):

Shuai Liu ◽

Hua Zhong ◽

Xiaoxi Meng ◽

Tong Sun ◽

Yangsheng Li ◽

...

Keyword(s):

Heavy Metal ◽

Candidate Genes ◽

Metal Contamination ◽

Core Collection ◽

Heavy Metal Contamination ◽

Agronomic Traits ◽

Association Studies ◽

P Value ◽

Genome Wide Association Studies ◽

Mini Core Collection

Abstract BackgroundRice is an important human staple food vulnerable to heavy metal contamination leading to serious concerns. High yield with low heavy metal contamination is a common but highly challenging goal for rice breeders worldwide due to lack of genetic knowledge and markers. ResultsTo identify candidate QTLs and develop molecular markers for rice yield and heavy metal content, a total of 191 accessions from the USDA Rice mini-core collection with over 3.2 million SNPs were employed to investigate the QTLs. Sixteen ionomic and thirteen agronomic traits were analyzed utilizing two univariate (GLM and MLM) and two multivariate (MLMM and FarmCPU) GWAS methods. 106, 47, and 97 QTLs were identified for ionomics flooded, ionomics unflooded, and agronomic traits, respectively, with the criterium of p-value <1.53×10-8, which was determined by the Bonferroni correction for p-value of 0.05. While 49 (~20%) of the 250 QTLs were coinciding with previous reported QTLs/genes, about 201 (~80%) were new. In addition, several new candidate genes involved in ionomic and agronomic traits control were identified by analyzing the DNA sequence, gene expression, and the homologs of the QTL regions. Our results further showed that each of the four GWAS methods can identify unique as well as common QTLs, suggesting that using multiple GWAS methods can complement each other in QTL identification, especially by combining univariate and multivariate methods. ConclusionsWhile 49 previously reported QTLs/genes were rediscovered, over 200 new QTLs for ionomic and agronomic traits were found in the rice genome. Moreover, multiple new candidate genes for agronomic and ionomic traits were identified. This research provides novel insights into the genetic basis of both ionomic and agronomic variations in rice, establishing the foundation for marker development in breeding and further investigation on reducing heavy-metal contamination and improving crop yields. Finally, the comparative analysis of the GWAS methods showed that each method has unique features and different methods can complement each other.

Download Full-text

Precision Mapping of a Maize MAGIC Population Identified a Candidate Gene for the Senescence-Associated Physiological Traits

Frontiers in Genetics ◽

10.3389/fgene.2021.716821 ◽

2021 ◽

Vol 12 ◽

Author(s):

Marlon Caicedo ◽

Eduardo D. Munaiz ◽

Rosa A. Malvar ◽

José C. Jiménez ◽

Bernardo Ordas

Keyword(s):

Candidate Gene ◽

Defense Mechanism ◽

Agronomic Traits ◽

Association Studies ◽

Recombinant Inbred Lines ◽

Sugar Transport ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Genome Wide ◽

Important Trait

Senescence is an important trait in maize (Zea mais L.), a key crop that provides nutrition values and a renewable source of bioenergy worldwide. Genome-wide association studies (GWAS) can be used to identify causative genetic variants that influence the major physiological measures of senescence, which is used by plants as a defense mechanism against abiotic and biotic stresses affecting its performance. We measured four physiological and two agronomic traits that affect senescence. Six hundred seventy-two recombinant inbred lines (RILs) were evaluated in two consecutive years. Thirty-six candidate genes were identified by genome-wide association study (GWAS), and 11 of them were supported by additional evidence for involvement in senescence-related processes including proteolysis, sugar transport, and sink activity. We identified a candidate gene, Zm00001d043586, significantly associated with chlorophyll, and independently studied its transcription expression in an independent panel. Our results showed that Zm00001d043586 affects chlorophyl rate degradation, a key determinant of senescence, at late plant development stages. These results contribute to better understand the genetic relationship of the important trait senescence with physiology related parameters in maize and provide new putative molecular markers that can be used in marker assisted selection for line development.

Download Full-text