Dataset Information

Genetic analysis and QTL mapping of the seed hardness trait in a black common bean (Phaseolus vulgaris) recombinant inbred line (RIL) population.

ABSTRACT: Seed hardness trait has a profound impact on cooking time and canning quality in dry beans. This study aims to identify the unknown genetic factors and associated molecular markers to better understand and tag this trait. An F_2:7 recombinant inbred line (RIL) population was derived from a cross between the hard and soft seeded black bean parents (H68-4 and BK04-001). Eighty-five RILs and the parental lines were grown at two locations in southern Manitoba during years 2014-2016. Seed samples were harvested manually at maturity to test for seed hardness traits. The hydration capacity and stone seed count were estimated by soaking the seeds overnight at room temperature following AACC method 56-35.01. Seed samples from 2016 tests were also cooked to determine effect of seed hardness on cooking quality. For mapping of genomic regions contributing to the traits, the RIL population was genotyped using the genotype by sequencing (GBS) approach. The QTL mapping revealed that in addition to the major QTL on chromosome 7 at a genomic location previously reported to affect seed-hydration, two novel QTL with significant effects were also detected on chromosomes 1 and 2. In addition, a major QTL affecting the visual appeal of cooked bean was mapped on chromosome 4. This multi-year-site study shows that despite large environmental effects, seed hardness is an oligo-genic and highly heritable trait, which is inherited independently of the cooking quality scored as visual appeal of cooked beans. The identification of the QTLs and development of SNP markers associated with seed hardness can be applied for common bean variety improvement and genetic exploitation of these traits.

SUBMITTER: Sandhu KS

PROVIDER: S-EPMC5842266 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Genetic analysis and QTL mapping of the seed hardness trait in a black common bean (<i>Phaseolus vulgaris</i>) recombinant inbred line (RIL) population.

Sandhu K S KS You F M FM Conner R L RL Balasubramanian P M PM Hou Anfu A

Molecular breeding : new strategies in plant improvement 20180223 3

Seed hardness trait has a profound impact on cooking time and canning quality in dry beans. This study aims to identify the unknown genetic factors and associated molecular markers to better understand and tag this trait. An F<sub>2:7</sub> recombinant inbred line (RIL) population was derived from a cross between the hard and soft seeded black bean parents (H68-4 and BK04-001). Eighty-five RILs and the parental lines were grown at two locations in southern Manitoba during years 2014-2016. Seed s ...[more]

PMID: 29568229

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Project description:Phenolic compounds present in common beans (Phaseolus vulgaris L.) have been reported to possess antimicrobial, anti-inflammatory and ultraviolet radiation (UVR) protective properties. UVR from sunlight, which consists of UV-B and UV-A radiations, induces reactive oxygen species (ROS) and free radical formation, consequently activating proteinases and enzymes such as elastase and tyrosinase, leading to premature skin aging. The objective of this work was to extract, characterize and evaluate the antioxidant and antiaging potential of polyphenols from a black bean endemic variety. The polyphenolic extract was obtained from black beans by supercritical fluid extraction (SFE) using CO2 with a mixture of water-ethanol as a cosolvent and conventional leaching with a mixture of water-ethanol as solvent. The polyphenolic extracts were purified and characterized, and antioxidant potential, tyrosinase and elastase inhibitory potentials were measured. The extract obtained using the SFE method using CO2 and H2O-Ethanol (50:50 v/v) as a cosolvent showed the highest total phenolic compounds yield, with 66.60 ± 7.41 mg GAE/g coat (p > 0.05) and 7.30 ± 0.64 mg C3GE/g coat (p < 0.05) of anthocyanins compared to conventional leaching. Nineteen tentative phenolic compounds were identified in leaching crude extract using ESI-QTOF. Quercetin-3-D-galactoside was identified in crude and purified extracts. The purified SFC extract showed IC50 0.05 ± 0.002 and IC50 0.21 ± 0.008 mg/mL for DPPH and ABTS, respectively. The lowest IC50 value of tyrosinase inhibition was 0.143 ± 0.02 mg/mL and 0.005 ± 0.003 mg/mL of elastase inhibition for leaching purified extract. Phenolic compounds presented theoretical free energy values ranging from -5.3 to -7.8 kcal/mol for tyrosinase and -2.5 to -6.8 kcal/mol for elastase in molecular docking (in silico) studies. The results suggest that the purified extracts obtained by SFE or conventional leaching extraction could act as antioxidant and antiaging ingredients for cosmeceutical applications.

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.

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Project description:BackgroundBean anthracnose is caused by the fungus Colletotrichum lindemuthianum (Sacc. & Magnus) Lams.- Scrib. Resistance to C. lindemuthianum in common bean (Phaseolus vulgaris L.) generally follows a qualitative mode of inheritance. The pathogen shows extensive pathogenic variation and up to 20 anthracnose resistance loci (named Co-), conferring resistance to specific races, have been described. Anthracnose resistance has generally been investigated by analyzing a limited number of isolates or races in segregating populations. In this work, we analyzed the response against eleven C. lindemuthianum races in a recombinant inbred line (RIL) common bean population derived from the cross Xana × Cornell 49242 in which a saturated linkage map was previously developed.ResultsA systematic genetic analysis was carried out to dissect the complex resistance segregations observed, which included contingency analyses, subpopulations and genetic mapping. Twenty two resistance genes were identified, some with a complementary mode of action. The Cornell 49242 genotype carries a complex cluster of resistance genes at the end of linkage group (LG) Pv11 corresponding to the previously described anthracnose resistance cluster Co-2. In this position, specific resistance genes to races 3, 6, 7, 19, 38, 39, 65, 357, 449 and 453 were identified, with one of them showing a complementary mode of action. In addition, Cornell 49242 had an independent gene on LG Pv09 showing a complementary mode of action for resistance to race 453. Resistance genes in genotype Xana were located on three regions involving LGs Pv01, Pv02 and Pv04. All resistance genes identified in Xana showed a complementary mode of action, except for two controlling resistance to races 65 and 73 located on LG Pv01, in the position of the previously described anthracnose resistance cluster Co-1.ConclusionsResults shown herein reveal a complex and specific interaction between bean and fungus genotypes leading to anthracnose resistance. Organization of specific resistance genes in clusters including resistance genes with different modes of action (dominant and complementary genes) was also confirmed. Finally, new locations for anthracnose resistance genes were identified in LG Pv09.

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Dataset Information

Genetic analysis and QTL mapping of the seed hardness trait in a black common bean (Phaseolus vulgaris) recombinant inbred line (RIL) population.

Publications

Genetic analysis and QTL mapping of the seed hardness trait in a black common bean (<i>Phaseolus vulgaris</i>) recombinant inbred line (RIL) population.

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