Dataset Information

Characterization of QTL and Environmental Interactions Controlling Flowering Time in Andean Common Bean (Phaseolus vulgaris L.).

ABSTRACT: Genetic variation for response of flowering time to photoperiod plays an important role in adaptation to environments with different photoperiods, and as consequence is an important contributor to plant productivity and yield. To elucidate the genetic control of flowering time [days to flowering (DTF); growing degree days (GDD)] in common bean, a facultative short-day plant, a quantitative trait loci (QTL) analysis was performed in a recombinant inbred mapping population derived from a cultivated accession and a photoperiod sensitive landrace, grown in different long-day (LD) and short-day (SD) environments by using a multiple-environment QTL model approach. A total of 37 QTL across 17 chromosome regions and 36 QTL-by-QTL interactions were identified for six traits associated with time to flowering and response to photoperiod. The DTF QTL accounted for 28 and 11% on average of the phenotypic variation in the population across LD and SD environments, respectively. Of these, a genomic region on chromosome 4 harboring the major DTF QTL was associated with both flowering time in LD and photoperiod response traits, controlling more than 60% of phenotypic variance, whereas a major QTL on chromosome 9 explained up to 32% of flowering time phenotypic variation in SD. Different epistatic interactions were found in LD and SD environments, and the presence of significant QTL × environment (QE) and epistasis × environment interactions implies that flowering time control may rely on different genes and genetic pathways under inductive and non-inductive conditions. Here, we report the identification of a novel major locus controlling photoperiod sensitivity on chromosome 4, which might interact with other loci for controlling common bean flowering time and photoperiod response. Our results have also demonstrated the importance of these interactions for flowering time control in common bean, and point to the likely complexity of flowering time pathways. This knowledge will help to identify and develop opportunities for adaptation and breeding of this legume crop.

SUBMITTER: Gonzalez AM

PROVIDER: S-EPMC7840541 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Characterization of QTL and Environmental Interactions Controlling Flowering Time in Andean Common Bean (<i>Phaseolus vulgaris</i> L.).

González Ana M AM Yuste-Lisbona Fernando J FJ Weller Jim J Vander Schoor Jacqueline K JK Lozano Rafael R Santalla Marta M

Frontiers in plant science 20210114

Genetic variation for response of flowering time to photoperiod plays an important role in adaptation to environments with different photoperiods, and as consequence is an important contributor to plant productivity and yield. To elucidate the genetic control of flowering time [days to flowering (DTF); growing degree days (GDD)] in common bean, a facultative short-day plant, a quantitative trait loci (QTL) analysis was performed in a recombinant inbred mapping population derived from a cultivate ...[more]

PMID: 33519852

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Project description:BackgroundGene-based (genic) microsatellites are a useful tool for plant genetics and simple sequence repeat loci can often be found in coding regions of the genome. While EST sequencing can be used to discover genic microsatellites, direct screening of cDNA libraries for repeat motifs can save on overall sequencing costs. The objective of this research was to screen a large cDNA library from and Andean common bean genotype for six di-nucleotide and tri-nucleotide repeat motifs through a filter hybridization approach and to develop microsatellite markers from positive clones.ResultsRobotics were used for high-throughput colony picking and to create a high-density filter of 18,432 double spotted cDNA clones which was followed by hybridization with repeat motif containing probes based on GA, CA, AAT, CAG, CAA and ACG repeats. A total of 1203 positive clones were identified by their addresses and sequenced from 5' ends and if required from 3' ends to confirm repeat motif and length. Out of 886 high quality sequences, 497 had complete microsatellite loci that were not truncated by the sequencing reaction and of these tri-nucleotide repeats were more common than di-nucleotide repeats. Different motifs were found in different frequencies in the 5' and 3' ends of the cDNAs. In a microsatellite development program, primers were designed for 248 SSR loci which were tested on a panel of 18 common bean genotypes to determine their potential as genetic markers finding higher average polymorphism information content for di-nucleotide repeat markers (0.3544) than for tri-nucleotide repeat markers (0.1536).ConclusionThe present study provides a set of validated gene-based markers for common bean that are derived from G19833, an Andean landrace that is an important source of disease and abiotic stress tolerance which has been used for physical map development and as a mapping parent. Gene-based markers appear to be very efficient at separating divergent wild and cultivated accessions as well as Andean and Mesoamerican gene pools and therefore will be useful for diversity analyses and for comparative and transcript mapping in common bean.

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.

Dataset Information

Characterization of QTL and Environmental Interactions Controlling Flowering Time in Andean Common Bean (Phaseolus vulgaris L.).

Publications

Characterization of QTL and Environmental Interactions Controlling Flowering Time in Andean Common Bean (<i>Phaseolus vulgaris</i> L.).

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