2012 Annual Report
1a.Objectives (from AD-416):
Objective 1: Identify genetic factors controlling bean seed processing quality and consumer acceptance attributes and identify QTL(s) for related traits including seed coat color and appearance, hardness, and digestibility.
Objective 2: Characterize genetic diversity for seed traits that influence human nutritional value of bean including antioxidant, mineral, and antinutrient levels that contribute to digestibility, and identify QTL(s) and gene(s) responsible for seed zinc accumulation.
1b.Approach (from AD-416):
Develop a linkage map for a black bean recombinant inbred line population using SSR and SNP markers. Use this resource identify QTL involved in canning quality and color retention in thermally processed beans, and to identify the Asp gene responsible for seed coat shine. Develop rapid phenotypic screens to for canning quality with near infrared spectroscopy. Measure variability for nutrient composition, cooking time, and sensory characteristics of modern and historically important dry bean varieties in the Mesoamerican gene pool. Develop populations of EMS mutagenized beans. Screen mutant populations for lines with reduced levels of seed raffinose and stachyose oligosaccharides. Screen diverse germplasm for natural variability in seed oligosaccharide content. Identify genes involved in seed zinc accumulation and tolerance to low zinc soils via transcriptome profiling, gene expression analysis, and molecular mapping.
Processing quality was evaluated on 108 black bean recombinant inbred lines that were grown in a replicated field experiment in 2011. The materials were canned and evaluated for color retention, texture, appearance and water uptake. A linkage map of 1500 single nucleotide polymorphism markers (SNP) and diversity array markers was developed for the black bean population. This map was anchored to the bean consensus map and the Phaseouls vulgaris genome sequence (v_0.9)(www.phytozome.net). The phenotypic data was used to conduct Quantitative Trait Loci (QTL) analysis of processing quality traits for which the data was collected over a 2 year field experiment (2010 and 2011). The QTL analysis revealed that the genomic region responsible for water uptake during soaking and processing of black beans is linked to the Asp gene for the shiny seed coat. QTL for color retention after canning, appearance, and anthocyanins content were also identified on chromosomes 5 and 11. Near-infrared analysis was conducted with seed from the 2010 and 2011 field seasons and evaluated as potential predictors of canning quality traits. The 2010 results have been analyzed, and it was found that NIR is able to predict water uptake whereas the prediction of other quality traits was not strong enough to warrant NIR as a method of selection. The analysis of 2011 materials is underway.
The evaluation of nutrient composition, including protein, fiber, folate, and minerals has been conducted on processed seed of 13 genotypes from 3 market classes grown over 2 years in Michigan. In addition, processing quality, including canned bean appearance, color, texture, and amylose/amylopectin content has been measured. Sensory panels have been used to evaluate how consumers rate the flavor, appearance, color, and texture of each of the cultivars. The data has been analyzed and the results of these studies are being written up for publication.
Mutagenized bean lines have been screened for seed oligosaccharide levels. In the first screening of 1000 lines, candidate lines were identified that were potentially low raffinose and/or low stachyose mutants. Based on second and third screening rounds, it appears that none of the lines with low oligosaccharide levels were heritable. Scientists will continue screening for natural variation for this trait in diverse bean germplasm.
Genetics of black bean processing quality. Black beans consumption has been increasing in the U.S. in recent years, often sold as a canned product. Processing quality is influenced by color leaching, and many times the product no longer appears black, but instead, an undesirable shade of brown. ARS scientists in East Lansing, Michigan have characterized genetic variability for color leaching in black beans. A black bean line with superior color retention was crossed to a line with inferior color retention. A linkage map was developed using 1500 molecular markers. The color retention and canning quality data was used in combination with the linkage map to identify regions of the bean genome important for processing quality. While it was previously believed that color retention in black bean is associated with seed coat shininess, ARS scientists found that not to be the case, which is good news for bean breeders since shiny beans are not favored by the canning industry. These findings will be useful in molecular plant breeding. In addition a bean line was identified with superior canning quality, color retention, and seed yield.
Sensory quality of historically important dry beans. Dry bean breeding efforts in the US began in the early 1900s and has focused on improving yields and agronomic characteristics while meeting strict consumer requirements for seed color, shape, and size expectations. Except for canning quality, other sensory characteristics of beans have not received as much attention by breeders. ARS scientists in East Lansing, Michigan evaluated the sensory quality, including flavor, appearance, and canning quality, of historically important bean varieties from different eras of three market classes. Canning quality has been consistently good in the five most important Navy bean varieties in the US since the 1900s and has improved in recent black bean varieties. Flavor is better in a new navy bean variety as compared to a foundational Navy landrace that precludes breeding. These findings are valuable to breeders interested in improving sensory attributes of their next generation of bean varieties.
Genetic control of essential dietary minerals in beans. Dry beans are a staple food in many parts of the world and are a valuable source of dietary zinc (Zn) and iron (Fe) for people who consume largely plant based diets. Different dry bean cultivars vary in seed zinc levels. ARS researchers in East Lansing, Michigan found that a total 24,427 genes were expressed in the pods, representing 79.5% of the total genes in the genome. A total of 467 genes had different expression patterns between two navy bean cultivars with 30% difference in seed zinc concentration. Ten of the differentially expressed genes are involved in Zn or Fe transport. This includes zinc-regulated transporter, iron regulated transporter like (ZIP), zinc-induced facilitator (ZIF) and yellow-stripe like (YSL) family genes. The identification of these differentially expressed Zn and Fe transport genes provide keys to genetic differences for seed mineral accumulation in dry bean which can be used to further increase seed Zn and Fe levels to benefit human nutrition.
Gelaeano, C.H., Fernandez, A.C., Franco-Herrera, N., Cichy, K.A., McClean, P.E., Vanderleyden, J., Beebe, S.E. 2011. Saturation of an intra-gene pool linkage map: toward unified consensus linkage map in common bean. PLoS One. 6(12):e28135.