ANNOUNCEMENT: Interested Members of the University Community are invited to attend the Final Oral Examination for the Degree of Doctor of Philosophy of 

Mohammad Erfatpour 

Of the Department of Plant Agriculture 

On Wednesday, March 31 at 2 PM Eastern Standard Time 

Via Zoom: Join Zoom Meeting Meeting ID: 958 7185 5218 Passcode: 356958 

Thesis title: Quantitative Trait Loci (QTL) and Candidate Gene Identification for the Non-Darkening Seed Coat Trait in Dry Beans (Phaseolus vulgaris L.) 

Advisory Committee                                        Examination Committee 

Dr. Peter Pauls, Advisor                                   Dr. Manju Misra, Chair 

Dr. Istvan Rajcan                                             Dr. Valerio Hoyos-Villegas, External examiner 

Dr. Lisa Duizer                                                Dr. Peter Pauls 

Dr. Gale Bozzo                                               Dr. Istvan Rajcan  

                                                                     Dr. Helen Booker 

ABSTRACT 

Seed coat colour is one of the main determinants of seed quality in commercial market classes of dry bean (Phaseolus vulgaris L.), including pinto bean. The beige background of the conventional pinto bean seed coat turns brown with age through a process known as postharvest seed coat darkening (PSCD). Beans with darkened seed coat are discounted in the market because they are perceived to be old, hard-to-cook beans. Seed coat darkening (SCD) is attributed to proanthocyanidin accumulation and its subsequent oxidation in the seed coat. Breeding for beans with reduced risk of PSCD has been given more attention in recent years because they are appealing to consumers and command higher prices in the market. To achieve this objective, it is important to understand the genetic control of the SCD trait and its relationship with other traits. J is a Mendelian genetic locus known to be responsible for SCD trait in dry beans in which the recessive allele produces a non-darkening (ND) seed coat phenotype. The main objectives of this thesis were to identify quantitative trait loci (QTL) and a gene associated with PSCD in dry beans and understand its function in promoting SCD. A mapping population consisting of 128 F_2:6 recombinant inbred lines (RILs) derived from a cross between a ND cranberry-like bean ‘Wit-rood boontje’ and a slow-darkening pinto bean ‘1533-15’ was characterized for seed coat phenotype and genotyped with an Illumina BARCBEAN6K_3 BeadChip. A major QTL was identified on chromosome Pv10 which explained 48% of the phenotypic variation for seed coat darkening. Amplicon sequencing of 21 candidate genes underlying the QTL revealed a single nucleotide deletion (c.703delG) in the candidate gene Phvul.010G130600 in ND RILs. In silico analysis indicated that Phvul.010G130600 encodes a protein with strong amino acid sequence identity (70%) to a R2R3-MYB-type transcription factor MtPAR, which has been shown to regulate proanthocyanidin biosynthesis in Medicago truncatula seed coat tissue. A gene-based dominant marker was developed for the dominant allele of Phvul.010G130600 which can be used for marker-assisted selection of ND beans. The ND seed coat trait was correlated with reduced grain yield; however, it is possible to develop high yielding ND lines. In comparison with the darkening genotypes, the ND genotypes were perceived as sweeter, and had softer and smoother texture and shorter cooking times. 

PUBLICATIONS 

Erfatpour M, Duizer L, Pauls KP (2021) Investigations of the effects of the non-darkening seed coat trait coded by the recessive jj alleles on agronomic, sensory, and cooking characteristics in pinto beans. Accepted in Crop Science https://doi.org/10.1002/csc2.20477 

Erfatpour M and Pauls KP (2020) A R2R3‑MYB gene‑based marker for the non‑darkening seed coat trait in pinto and cranberry beans (Phaseolus vulgaris L.) derived from ‘Wit‑rood boontje’. Theoretical and Applied Genetics doi: 10.1007/s00122-020-3571-7 

Erfatpour M, Navabi A, Pauls KP (2018) Mapping the non-darkening trait from ‘Wit-rood boontje’ in bean (Phaseolus vulgaris). Theoretical and Applied Genetics doi: 10.1007/s00122-018-3081-y