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QTL Mapping of Seed Quality Traits Including Cooking Time, Flavor, and Texture in a Yellow Dry Bean (Phaseolus vulgaris L.) Population.

ABSTRACT: Manteca yellow dry beans (Phaseolus vulgaris L.) have many quality traits that appeal to consumers, including fast cooking times, creamy texture, and sweet, buttery flavor. They are native to Chile and consumed in regions of South America and Africa but are largely unfamiliar to United States consumers. While cooking time, flavor, and texture have not been prioritized in United States dry bean breeding programs, genetic variability exists such that these traits could be addressed through breeding. In this study, a recombinant inbred line (RIL) population was developed from a cross between Ervilha (Manteca) and PI527538 (Njano), yellow dry beans with contrasting cooking time and sensory attributes. The population and parents were grown for 2 years in Michigan and evaluated for cooking time and sensory attribute intensities, including total flavor, beany, vegetative, earthy, starchy, sweet, bitter, seed-coat perception, and cotyledon texture. Cooking time ranged 19-34 min and exhibited high broad-sense heritability (0.68). Sensory attribute intensities also exhibited variation among RILs, although broad-sense heritability was low, with beany and total flavor exhibiting the highest (0.33 and 0.27). A linkage map of 870 single nucleotide polymorphisms markers across 11 chromosomes was developed for quantitative trait loci (QTL) mapping, which revealed QTL for water uptake (3), cooking time (6), sensory attribute intensities (28), color (13), seed-coat postharvest non-darkening (1), seed weight (5), and seed yield (2) identified from data across 2 years. Co-localization was identified for starchy, sweet, and seed-coat perception on Pv01; for total flavor, beany, earthy, starchy, sweet, bitter, seed-coat perception, cotyledon texture, and color on Pv03; water uptake and color on Pv04; total flavor, vegetative, sweet, and cotyledon texture on Pv07; cooking time, starchy, sweet, and color on Pv08; and water uptake, cooking time, total flavor, beany, starchy, bitter, seed-coat perception, cotyledon texture, color, and seed-coat postharvest non-darkening on Pv10. The QTL identified in this work, in particular CT8.2 and CT10.2, can be used to develop molecular markers to improve seed quality traits in future dry bean varieties. Considering yellow dry beans already excel in quality and convenience, they might be an ideal market class to signal a new focus on consumer-valued traits in the United States.

SUBMITTER: Bassett A

PROVIDER: S-EPMC8259628 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Cooking time of the common bean is an important trait for consumer preference, with implications for nutrition, health, and environment. For efficient germplasm improvement, breeders need more information on the genetics to identify fast cooking sources with good agronomic properties and molecular breeding tools. In this study, we investigated a broad genetic variation among tropical germplasm from both Andean and Mesoamerican genepools. Four populations were evaluated for cooking time (CKT), water absorption capacity (WAC), and seed weight (SdW): a bi-parental RIL population (DxG), an eight-parental Mesoamerican MAGIC population, an Andean (VEF), and a Mesoamerican (MIP) breeding line panel. A total of 922 lines were evaluated in this study. Significant genetic variation was found in all populations with high heritabilities, ranging from 0.64 to 0.89 for CKT. CKT was related to the color of the seed coat, with the white colored seeds being the ones that cooked the fastest. Marker trait associations were investigated by QTL analysis and GWAS, resulting in the identification of 10 QTL. In populations with Andean germplasm, an inverse correlation of CKT and WAC, and also a QTL on Pv03 that inversely controls CKT and WAC (CKT3.2/WAC3.1) were observed. WAC7.1 was found in both Mesoamerican populations. QTL only explained a small part of the variance, and phenotypic distributions support a more quantitative mode of inheritance. For this reason, we evaluated how genomic prediction (GP) models can capture the genetic variation. GP accuracies for CKT varied, ranging from good results for the MAGIC population (0.55) to lower accuracies in the MIP panel (0.22). The phenotypic characterization of parental material will allow for the cooking time trait to be implemented in the active germplasm improvement programs. Molecular breeding tools can be developed to employ marker-assisted selection or genomic selection, which looks to be a promising tool in some populations to increase the efficiency of breeding activities.

Project description:Common bean productivity is reduced by several abiotic stress factors like drought and low soil fertility, leading to yield losses particularly in low input smallholder farming systems in the tropics. To understand the genetics of stress tolerance, and to improve adaptation of common bean to adverse environments, the BAT 881 x G21212 population of 95 recombinant inbred lines (RILs) was evaluated under different abiotic stress conditions in 15 trials across four locations in Colombia, representing two higher altitude (Darién, Popayán) and two lower altitude (Palmira, Quilichao) locations. Stress vs non-stress treatments showed that yields were reduced in drought trials in Palmira by 13 and 31%, respectively, and observed yield reductions in low phosphorus stress were 39% in Quilichao, 16% in Popayán, and 71% in Darién, respectively. Yield components and biomass traits were also reduced. Traits linked to dry matter redistribution from stems, leaves and pods to seed, such as pod harvest index and total non-structural carbohydrates, were found to be important factors contributing to yield in all conditions. In contrast, early maturity was correlated with improved yield only in lower altitude locations, whereas in higher altitudes delayed maturity promoted yield. Superior RILs that combine stress tolerance and high cross-location productivity were identified. Lines that showed good yield under strong stress conditions also performed well under non-stress conditions, indicating that breeder's selection can be applied for both conditions at the same time. Quantitative trait loci (QTL) analyses revealed a stable yield QTL on chromosome Pv04, detected individually in all locations, several stress treatments and in best linear unbiased predictions (BLUPs) across all trials. Furthermore, two QTL hotspots for maturity traits were identified on Pv01 and Pv08, which are the most stable QTL. The constitutive yield QTL could serve as a good candidate for marker development and could be used in marker assisted selection. Increased understanding of the physiology of abiotic stress tolerance, combined with the availability of superior germplasm and molecular tools, will aid breeding efforts for further improvement of these plant traits.

Project description:BackgroundCommon bean (Phaseolus vulgaris L.) is the most important grain legume for human diet worldwide and the angular leaf spot (ALS) is one of the most devastating diseases of this crop, leading to yield losses as high as 80%. In an attempt to breed resistant cultivars, it is important to first understand the inheritance mode of resistance and to develop tools that could be used in assisted breeding. Therefore, the aim of this study was to identify quantitative trait loci (QTL) controlling resistance to ALS under natural infection conditions in the field and under inoculated conditions in the greenhouse.ResultsQTL analyses were made using phenotypic data from 346 recombinant inbreed lines from the IAC-UNAxCAL 143 cross, gathered in three experiments, two of which were conducted in the field in different seasons and one in the greenhouse. Joint composite interval mapping analysis of QTLxenvironment interaction was performed. In all, seven QTLs were mapped on five linkage groups. Most of them, with the exception of two, were significant in all experiments. Among these, ALS10.1DG,UC presented major effects (R2 between 16%-22%). This QTL was found linked to the GATS11b marker of linkage group B10, which was consistently amplified across a set of common bean lines and was associated with the resistance. Four new QTLs were identified. Between them the ALS5.2 showed an important effect (9.4%) under inoculated conditions in the greenhouse. ALS4.2 was another major QTL, under natural infection in the field, explaining 10.8% of the variability for resistance reaction. The other QTLs showed minor effects on resistance.ConclusionsThe results indicated a quantitative inheritance pattern of ALS resistance in the common bean line CAL 143. QTL x environment interactions were observed. Moreover, the major QTL identified on linkage group B10 could be important for bean breeding, as it was stable in all the environments. Thereby, the GATS11b marker is a potential tool for marker assisted selection for ALS resistance.

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QTL Mapping of Seed Quality Traits Including Cooking Time, Flavor, and Texture in a Yellow Dry Bean (Phaseolus vulgaris L.) Population.

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