Marker-based linkage map of Andean common bean (Phaseolus vulgarisL.) and mapping of QTLs underlying popping ability traits

Abstract

BackgroundNuña bean is a type of ancient common bean (Phaseolus vulgaris L.) native to the Andean region of South America, whose seeds possess the unusual property of popping. The nutritional features of popped seeds make them a healthy low fat and high protein snack. However, flowering of nuña bean only takes place under short-day photoperiod conditions, which means a difficulty to extend production to areas where such conditions do not prevail. Therefore, breeding programs of adaptation traits will facilitate the diversification of the bean crops and the development of new varieties with enhanced healthy properties. Although the popping trait has been profusely studied in maize (popcorn), little is known about the biology and genetic basis of the popping ability in common bean. To obtain insights into the genetics of popping ability related traits of nuña bean, a comprehensive quantitative trait loci (QTL) analysis was performed to detect single-locus and epistatic QTLs responsible for the phenotypic variance observed in these traits.ResultsA mapping population of 185 recombinant inbred lines (RILs) derived from a cross between two Andean common bean genotypes was evaluated for three popping related traits, popping dimension index (PDI), expansion coefficient (EC), and percentage of unpopped seeds (PUS), in five different environmental conditions. The genetic map constructed included 193 loci across 12 linkage groups (LGs), covering a genetic distance of 822.1 cM, with an average of 4.3 cM per marker. Individual and multi-environment QTL analyses detected a total of nineteen single-locus QTLs, highlighting among them the co-localized QTLs for the three popping ability traits placed on LGs 3, 5, 6, and 7, which together explained 24.9, 14.5, and 25.3% of the phenotypic variance for PDI, EC, and PUS, respectively. Interestingly, epistatic interactions among QTLs have been detected, which could have a key role in the genetic control of popping.ConclusionsThe QTLs here reported constitute useful tools for marker assisted selection breeding programs aimed at improving nuña bean cultivars, as well as for extending our knowledge of the genetic determinants and genotype x environment interaction involved in the popping ability traits of this bean crop.

Uncovering the genetic architecture of Colletotrichum lindemuthianum resistance through QTL mapping and epistatic interaction analysis in common bean

“…The genetic linkage map described by Yuste-Lisbona et al ( 2012 ) was used for QTL analysis. The SCAR SW13 and SW12 (Fourie et al, 2004 ; Rodríguez-Suárez et al, 2008 ), 1 AFLP, 3 SSR, 29 SNP, and the seed coat color gene ( P ) were added to this map, which finally consisted of 229 loci (86 AFLP, 98 SSR, 42 SNP, 2 SCAR, and P locus) distributed on 11 LGs.…”

QTL Mapping for Drought-Responsive Agronomic Traits Associated with Physiology, Phenology, and Yield in an Andean Intra-Gene Pool Common Bean Population

“…Inter-genepool crosses enable high coverage of the genetic map with polymorphic markers between Andean and Mesoamerican genepools and were utilized to detect phenological and seed mass QTLs associated with drought tolerance [10]. On the other hand QTLs identified in an intra-genepool population can be easier to transfer to plants within the same gene pool; however, because of a more similar genetic makeup, the development of genetic linkage maps is limited by lower numbers of polymorphic markers [11][12][13][14]. Mesoamerican mapping population has been utilized to identify drought tolerance-associated QTL for phenological and yield-related traits [15], as well as QTL for photosynthate acquisition, accumulation, and remobilization traits in drought stress [16].…”

“…Mesoamerican mapping population has been utilized to identify drought tolerance-associated QTL for phenological and yield-related traits [15], as well as QTL for photosynthate acquisition, accumulation, and remobilization traits in drought stress [16]. Although Andean genetic maps have previously been utilized to detect QTL associated with complex traits with polygenic inheritance, such as popping ability [14], only recently has QTL mapping of drought-responsive traits been reported [9]. In this particular study, a population derived from drought-tolerant Ecuadorian cultivar Portillo was used for mapping of phenology, yield component, and partitioning traits in field trials in Uganda [9].…”

Breeding Annual Grain Legumes for Sustainable Agriculture: New Methods to Approach Complex Traits and Target New Cultivar Ideotypes

“…The nutritional features of popped/roasted seeds make them a healthy low fat and high protein snack. Although the popping trait has been profusely studied in maize (popcorn), little is known about the biology and genetic basis of the popping/roasting ability in common bean (Yuste-Lisbona et al, 2012).…”

“…Many quality traits are quantitative (Diaz et al, 2010) and somewhat influenced by the environment (Blair et al, 2009), but the molecular basis of the quality interactions has not been clarified yet. Several QTL studies for individual quality traits were performed in common bean, such as color retention after processing (Wright and Kelly, 2011), iron and zinc seed concentration (Blair et al, 2010(Blair et al, , 2011, water absorption and coat proportion (Pérez-Vega et al, 2010), water absorption and cooking time (Vasconcelos Garcia et al, 2012), and more recently, seed phytate and phosphorus content or nuña bean popping/roasting ability (Yuste-Lisbona et al, 2012). In some cases candidate genes have been identified or at least associated molecular markers developed to use on QTL assisted selection.…”