Project Number: 2090-21220-001-04-R
Project Type: Reimbursable Cooperative Agreement
Start Date: Oct 1, 2013
End Date: Aug 31, 2017
Pinto bean (Phaseolus vulgaris L.) is the most economically important dry bean grown in the United States. This crop has undergone a dramatic restructuring of its architecture from a prostate Type III growth habit to an upright Type II growth habit in the last 20 years. The new Type II pinto bean is now the standard for the industry because it permits direct harvesting. Because of the yet to be discovered genetic nature of the Type II phenotype, pinto breeders now primarily focus on crosses within that growth habit. Yet, the transition has not been without a cost. Important traits, for example earliness, that were the result of 50 years of pinto bean improvement, have been lost or not yet fully recovered in Type II beans. The goal of this project is to develop an effective, modern breeding strategy that facilitates the rapid recovery of those beneficial Type III alleles of high strategic value for bean breeders. This project proposes to scan the genomes of Type II and Type III pinto beans to identify regions that are distinct to each. These genomic locations will then be genetically correlated with those phenotypic traits that distinguish the two pinto classes. Those discoveries will then facilitate the development of a suite of markers that effectively monitor the transition of the lost Type III traits into the modern Type II pinto germplasm. Specific objectives of this project are to: i) identify the genomic fingerprint for the desired dry bean ideotype, and ii) determine if genomic markers can be used to facilitate breeding for bean ideotype.
An initial set of 15 single crosses will be conducted among pinto beans based on data obtained from a 5K SNP chip from the BeanCAP project and GBS data generated from this project. Crosses will include pinto genotypes from both type II and type III. Most crosses will be among types, but crosses between type II genotypes will be also included since this is what most breeding programs are currently using in their breeding schemes. Given the phenotyipic and genotypic segregation observed in these populations, a subset of crosses will be selected for the breeding effort. Crosses will be then divided into two parallel sets: for a given cross, half of the population will be selected based on the "genomic ideotype" previously defined and the other half will follow regular “phenotypic selection” as it is normally done in a breeding program (using a pedigree method). The phenotypic selection will be made at 2 locations (North Dakota and Washington) while the genotypic selection will be made in the lab at NDSU but the populations will be grown together in the field every growing season. Selection will be practiced on each generation from F2 to F5. For each generation, the following phenotypic traits will be measured in 3 plants per line at different plant stages: hypocotyl length, days to flower and maturity, plant height, lowest pod height, branch angle, number of pods and distribution, and plot yield and seed weight. However, seed yield and harvest losses will be measured only at the final generations (F5-F6) once enough seed of the breeding lines is available and they have reached a higher level of homozygosity. Once all data is collected, a side by side comparison of the ideotypes produced will be made using all the traits measured. In addition, the phenotypic data will be used to improve the genomic ideotype originally defined with the objective of gaining accuracy on the genomic prediction model.