Dissertation/Thesis Abstract

Toward Genomics-based Breeding in Phaseolus vulgaris and Quantitative Trait Locus Mapping of Angular Leaf Spot Resistance
by Miller, Tamara Iva, Ph.D., University of California, Davis, 2019, 106; 13428184
Abstract (Summary)

The common bean (Phaseolus vulgaris L.) is consumed by millions of people worldwide and is a staple source of protein, starch and micronutrients. Common bean production across the world is affected by abiotic and biotic stresses that limit the growth and yield of this important crop. Efforts to breed improved common bean for dissemination to farmers and consumers in East Africa is underway in several breeding programs worldwide. Improvement on agronomic and consumer traits such as disease resistance can be greatly aided by the application of next generation sequencing technologies. With the decreasing cost of DNA sequencing, genomic re-sequencing of diverse common bean accessions facilitates marker- assisted breeding that can be used to speed the creation of new common bean cultivars.

Marker-assisted selection (MAS) is an important aspect of modern bean breeding that seeks to utilize genetic markers to select individuals with improved agronomic and consumer traits. For example, breeders in the African Bean Consortium seek to introgress known genetic loci conferring resistance to multiple diseases into bean genetic backgrounds with preferred seed and agronomic characteristics. However, the usefulness of markers is dependent on whether they are polymorphic in the specific parents of the breeding program. Often genetic markers identified in a specific plant population are not useful for marker assisted selection among a different set of bean parents, which necessitates identification of novel markers linked to the genes of interest that are polymorphic among breeding parents.

One disease that greatly affects common bean production in humid tropical and sub-tropical growing regions is Angular Leaf Spot (ALS; caused by the foliar fungus Pseudocercospora griseola Sacc.). Marker assisted breeding is being used in multiple different bean breeding programs to improve the resistance of adapted cultivars to ALS. The ALS resistance locus, Phg-2, is an important resistance locus used to improve plant resistance to Angular Leaf Spot in South America and Pan Africa, however in the case of the African Bean Consortium breeding programs in East Africa, certain bean parents used for breeding were monomorphic for the original marker used to perform marker assisted selection of Phg-2. In order to facilitate marker assisted selection of Phg-2 in specific breeding parents used in the Uganda bean improvement program, an alternative, co-dominant, marker linked to the Phg-2 ALS resistance locus was developed (Chapter 1). A new marker, g796, was identified which is polymorphic among the breeding parents; its co-segregation was confirmed in a segregating F2 population derived from the cross between French bean variety Amy and the ALS resistance donor, Mexico 54. This work was conducted in collaboration with Stephen Kimno and Esther Arunga at Embu University, Kenya, as well as other members of the African Bean Consortium bean breeding programs in Tanzania, Uganda, and Ethiopia.

The application of DNA sequencing to marker-assisted breeding and crop improvement is rapidly becoming common in the development of improved bean varieties. A nearly complete reference genome and transcriptome for Phaseolus vulgaris was released in 2014 and newly resequenced genomes of diverse bean accessions are being developed for the purpose of marker assisted breeding. In Chapter 2, whole-genome resequencing of 29 bean accessions, including accessions commonly used as breeding parents, was carried out in collaboration with the Ratz lab at the International Center for Tropical Agriculture (CIAT, Colombia). Genetic diversity analysis was performed in order to access the evolutionary relationships between the sequenced bean genomes. Data generated by this work was made available to the larger bean research community and will be used by breeders and geneticists to perform marker-assisted selection and genetic analysis in the future.

Angular leaf spot (ALS) occurs throughout Eastern and Southern Africa (as well as other parts of the world) and can cause yield losses up to 80% in environments that favor the disease. ALS is caused by the fungal pathogen, Pseudocercospora griseola, a highly diverse pathogen with many different races that infect diverse types of bean hosts. Growing crop cultivars with genetic resistance to the disease is one of the most effective measures for farmers to reduce crop losses due to ALS. The landrace Mexico 54 is used as a donor for ALS resistance in East Africa and marker-assisted selection of the Phg-2 ALS resistance locus from Mexico 54 is underway in multiple breeding programs in order to increase the resistance of adapted bean germplasm in East Africa and Brazil. Previous allelism tests between different ALS resistance donors suggested additional resistance loci exist in Mexico 54 besides the Phg-2 locus and were named Phg-5 and Phg-6. The genomic locations of the proposed Phg-5 and Phg-6 resistance genes in Mexico 54 have never been investigated, however, the existence of multiple resistance loci in Mexico 54 is likely the cause of its high level of resistance to ALS on multiple continents. In Chapter 3, a biparental mapping population consisting of 167 F8 recombinant inbred lines (RIL) was derived from a cross between Kablanketi, a preferred bean market type in Tanzania, and Mexico 54 in order to map additional quantitative trait loci that confer resistance to ALS in Mexico 54. The identification of novel ALS resistance loci will aid breeders to develop resistant cultivars as well as provide a greater understanding of the genetic diversity that influences resistance to ALS.

Indexing (document details)
Advisor: Gepts, Paul L.
Commitee: Bostock, Richard, Melotto, Maeli
School: University of California, Davis
Department: Horticulture and Agronomy
School Location: United States -- California
Source: DAI-B 81/2(E), Dissertation Abstracts International
Subjects: Genetics, Agriculture, Plant sciences
Keywords: Angular Leaf Spot, Common Bean, Genomics, Phaselolus vulgaris, Plant Breeding, Plant Pathology
Publication Number: 13428184
ISBN: 9781085732857
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