Nested Association Mapping of Stem Rust Resistance in Wheat Using Genotyping by Sequencing

Bajgain, Prabin; Rouse, Matthew N.; Tsilo, Toi J.; Macharia, Godwin; Bhavani, Sridhar; Jin, Yue; Anderson, James A.

doi:10.1371/journal.pone.0155760

Cited by 109 publications

(93 citation statements)

References 80 publications

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“…Recently, the national program collaborating with other researchers has implemented both biparental and association mapping works for rust resistance genes (e.g., [23,33,34]). Such effort will contribute to faster cultivar development.…”

Section: Leveraging Modern Breeding Tools and Best Practicesmentioning

confidence: 99%

Wheat in Kenya: Past and Twenty-First Century Breeding

Macharia¹,

Ngina²

2017

Wheat Improvement, Management and Utilization

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Plant breeders aim to improve crop varieties to benefit humankind. Since wheat was introduced in Kenya, numerous varieties have been released and cultivated to varying extents. Past genetic gains have been fragile due to various environmental challenges-mostly rust diseases, and unfavorable socio-economic national policy for the crop. The role and the contribution of wheat breeding to the success of the crop in Kenya for over a century is reviewed. It is considered that systematic exploitation of local and introduced genetic diversity has contributed to release of varieties with superior genetics over time, enhancing productivity from 1 ton/ha in the 1920's to approximately 3 tons/ha recently. Consistent rise in demand to about 1 million metric tons suggests that the national wheat breeding research program must be remodeled to leverage modern tools and best practices; to reconsider its target range of breeding environments in the wake of climate change; to entrench its engagement with the international wheat research programs; and to promote a culture of continuous mentorship. Here, cases are highlighted where the national program has moved in such positive directions to address the varietal needs of a crop that has fully integrated in the economy and the diets of many Kenyans.

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Section: Leveraging Modern Breeding Tools and Best Practicesmentioning

confidence: 99%

Wheat in Kenya: Past and Twenty-First Century Breeding

Macharia¹,

Ngina²

2017

Wheat Improvement, Management and Utilization

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“…Sr2/ Yr30/Lr27/Pbc1, Sr55/Lr67/Yr46/Pm46/Ltn3, Sr57/Lr34/Yr18/Pm38/Ltn1 and Sr58/ Lr46/Yr29/Pm39/Ltn2 (William et al 2006;Lillemo et al 2008;Krattinger et al 2009;Mago et al 2011a;Herrera-Foessel et al 2014;Kolmer et al 2015). Several Kenyan cultivars have been shown to be good sources of APR genes controlling stem rust (Knott 1968;Njau et al 2009Njau et al , 2010Onguso and Njau 2015;Bajgain et al 2016).…”

Section: Cereal Research Communicationsmentioning

confidence: 99%

“…Eight Kenyan bread wheat cultivars (Gem, Romany, Paka, Fahari, Kudu, Pasa, Ngiri and Popo) with known stem rust resistance (Njau et al 2009;Bajgain et al 2016), together with four local checks (Kariega, Morocco, McNair and SST88) were used for the study. Seeds of the cultivars were obtained from the National Small Grain Germplasm Collection of the Agricultural Research Council-Small Grain Institute (ARC-SGI) in Bethlehem.…”

Section: Plant Materials and Seedling Screeningmentioning

confidence: 99%

“…The cultivars used for the crosses were chosen because of their known resistance to wheat diseases, acceptable end-use quality and yield. Kenyan cultivars also carry many Sr genes (McIntosh et al 1995;Njau et al 2009Njau et al , 2010Bajgain et al 2016), hence the strategic inclusion of these cultivars in the study. Table 2 shows the characteristics of each cultivar used to develop the nested bi-parental population.…”

Section: Development Of a Nested Bi-parental Populationmentioning

confidence: 99%

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Adult plant resistance of selected Kenyan wheat cultivars to leaf rust and stem rust diseases

Figlan¹,

Baloyi²,

Hlongoane³

et al. 2017

Cereal Research Communications

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Phenotypic and genotypic evaluation of wheat genetic resources and development of segregating populations are pre-requisites for identifying rust resistance genes. The objectives of this study were to assess adult plant resistance (APR) of selected wheat genotypes to leaf rust and stem rust and to develop segregating populations for resistance breeding. Eight selected Kenyan cultivars with known resistance to stem rust, together with local checks were evaluated for leaf rust and stem rust resistance at seedling stage and also across several environments. Selected diagnostic markers were used to determine the presence of known genes. All eight cultivars were crossed with local checks using a bi-parental mating design. Seedling tests revealed that parents exhibited differential infection types against wheat rust races. Cultivars Paka and Popo consistently showed resistant infection types at seedling stage, while Gem, Romany, Pasa, Fahari, Kudu, Ngiri and Kariega varied for resistant and susceptible infection types depending on the pathogen race used. The control cultivars Morocco and McNair consistently showed susceptible infection types as expected. In the field, all cultivars except for Morocco showed moderate to high levels of resistance, indicating the presence of effective resistance genes. Using diagnostic markers, presence of Lr34 was confirmed in Gem, Fahari, Kudu, Ngiri and Kariega, while Sr2 was present in Gem, Romany, Paka and Kudu. Seedling resistance gene, Sr35, was only detected in cultivar Popo. Overall, the study developed 909 F 6:8 recombinant inbred lines (RILs) as part of the nested mating design and are useful genetic resources for further studies and for mapping wheat rust resistance genes.

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“…Marcotuli et al (2016), Körber et al (2016), Liu et al (2016)] , and genotyping-by-sequencing [GBS; e.g. Bajgain et al (2016), Boutet et al (2016), Yu et al (2016)]. Sequencing technologies also have been used to understand domestication events (Henry 2012), mechanisms of biological and molecular processes within the cell, and whole genome duplication events [e.g.…”

Section: High Throughput Sequencing Technologymentioning

confidence: 99%

Genomic characterisation of Australian wild rice species

Brożyńska¹

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Rice (Oryza sativa L.) is one of the most important crops in the world and a basic food source for about two-thirds of the population. It has been grown in the tropics and sub-tropics probably for thousands of years. Owing to the fast growing world population, there is a high demand for increased and improved rice production. Wild relatives of cultivated rice, the related A genome species, carry a vast genetic diversity and are a significant resource for rice improvement. including the cultivars, using full chloroplast sequence as well as nuclear genome regions; secondly, creating genomic resources of these wild rice relatives by means of whole genome sequencing and generating reference genomes for the two novel Australian wild rice taxa. The draft genomes generated were used for whole genome characterization studies including phylogenetic reconstruction with high resolution, divergence time estimation, structural descriptions, gene annotation, and repeat content exploration. The evolutionary inference results revealed that northern

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Nested Association Mapping of Stem Rust Resistance in Wheat Using Genotyping by Sequencing

Cited by 109 publications

References 80 publications

Wheat in Kenya: Past and Twenty-First Century Breeding

Wheat in Kenya: Past and Twenty-First Century Breeding

Adult plant resistance of selected Kenyan wheat cultivars to leaf rust and stem rust diseases

Genomic characterisation of Australian wild rice species

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