A review of breeding objectives, genomic resources, and marker-assisted methods in common bean (Phaseolus vulgaris L.) (original) (raw)
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Euphytica, 2009
Common bean (Phaseolus vulgaris L.) improvement programs have been successful using conventional breeding methods to accomplish a wide array of important objectives. Specific achievements include the extension of range of adaptation of the crop, the development of cultivars with enhanced levels of disease and pest resistance and breeding lines that possess greater tolerance to drought. The most effective breeding method depends on the expression and inheritance of the trait to be selected and the target environment. Many bean improvement programs use molecular markers to facilitate cultivar development. In fact, several recent germplasm releases have used molecular markers to introgress and or pyramid major genes and QTL for disease resistance. Related species (P. coccineus and P. acultifolius) via interspecific hybridizations remain an important albeit long-term source for resistance to economically important diseases. Slow progress has been made in the improvement of traits such as adaptation to low soil fertility and tolerance to high levels of soluble Al in the soil using conventional breeding methods. The inability to directly measure root traits and the importance of genotype 9 environment interaction complicate the selection of these traits. In addition, symbiotic relationships with Rhizobium and mycorrhiza need to be taken into consideration when selecting for enhanced biological N fixation and greater or more efficient acquisition of soil P. Genomic examination of complex traits such as these should help bean breeders devise more effective selection strategies. As integration of genomics in plant breeding advances, the challenge will be to develop molecular tools that also benefit breeding programs in developing countries. Transgenic breeding methods for bean improvement are not well defined, nor efficient, as beans are recalcitrant to regeneration from cell cultures. Moreover, if issues related to consumer acceptance of GMOs cannot be resolved, traits such as herbicide tolerance in transgenic bean cultivars which would help farmers reduce production costs and decrease soil erosion will remain unrealized.
Genetic Resources and Crop Evolution
Common bean (Phaseolus vulgaris L.) is an important staple crop for smallholder farmers, particularly in Eastern and Southern Africa. To support common bean breeding and seed dissemination, a high throughput SNP genotyping platform with 1500 established SNP assays has been developed at a genotyping service provider which allows breeders without their own genotyping infrastructure to outsource such service. A set of 708 genotypes mainly composed of germplasm from African breeders and CIAT breeding program were assembled and genotyped with over 800 SNPs. Diversity analysis revealed that both Mesoamerican and Andean gene pools are in use, with an emphasis on large seeded Andean genotypes, which represents the known regional preferences. The analysis of genetic similarities among germplasm entries revealed duplicated lines with different names as well as distinct SNP patterns in identically named samples. Overall, a worrying number of inconsistencies was identified in this data set of very diverse origins. This exemplifies the necessity to develop and use a cost-effective fingerprinting platform to ensure germplasm purity for research, sharing and seed dissemination. The genetic data also allows to visualize introgressions, to identify heterozygous regions to evaluate hybridization success and to employ marker-assisted selection. This study presents a new resource for the common bean community, a Electronic supplementary material The online version of this article (
Frontiers in Plant Science
Phaseolus vulgaris L., known as common bean, is one of the most important grain legumes cultivated around the world for its immature pods and dry seeds, which are rich in protein and micronutrients. Common bean offers a cheap food and protein sources to ameliorate food shortage and malnutrition around the world. However, the genetic basis of most important traits in common bean remains unknown. This study aimed at identifying QTL and candidate gene models underlying twenty-six agronomically important traits in common bean. For this, we assembled and phenotyped a diversity panel of 200 P. vulgaris genotypes in the greenhouse, comprising determinate bushy, determinate climbing and indeterminate climbing beans. The panel included dry beans and snap beans from different breeding programmes, elite lines and landraces from around the world with a major focus on accessions of African, European and South American origin. The panel was genotyped using a cost-conscious targeted genotyping-by-...
Genomics of Phaseolus Beans, a Major Source of Dietary Protein and Micronutrients in the Tropics
Common bean is grown and consumed principally in developing countries in Latin America, Africa, and Asia. It is largely a subsistence crop eaten by its producers and, hence, is underestimated in production and commerce statistics. Common bean is a major source of dietary protein, which complements carbohydrate-rich sources such as rice, maize, and cassava. It is also a rich source of minerals, such as iron and zinc, and certain vitamins. Several large germplasm collections have been established, which contain large amounts of genetic diversity, including the five domesticated Phaseolus species and wild species, as well as an incipient stock collection. The genealogy and genetic diversity of P. vulgaris are among the best known in crop species through the systematic use of molecular markers, from seed proteins and isozymes to simple sequence repeats, and DNA sequences. Common bean exhibits a high level of genetic diversity, compared with other selfing species. A hierarchical organization into gene pools and ecogeographic races has been established. There are over 15 mapping populations that have been established to study the inheritance of agronomic traits in different locations. Most linkage maps have been correlated with the core map established in the BAT93 x Jalo EEP558 cross, which includes several hundreds of markers, including Restriction Fragment Length Polymorphisms, Random Amplified Polymorphic DNA, Amplified Fragment Length Polymorphisms, Short Sequence Repeats, Sequence Tagged Sites, and Target Region Amplification Polymorphisms. Over 30 individual genes for disease resistance and some 30 Quantitative Trait Loci for a broad range of agronomic traits have been tagged. Eleven BAC libraries have been developed in genotypes that represent key steps in the evolution before and after domestication of common bean, a unique resource among crops. Fluorescence in situ hybridization provides the first links between chromosomal and genetic maps. A gene index based on some P. vulgaris 21,000 expressed sequence tags (ESTs) has been developed. ESTs were developed from different genotypes, organs, and physiological conditions. They resolve currently in some 6,500–6,800 singletons and 2,900 contigs. An additional 20,000 embryonic P. coccineus ESTs provides an additional resource. Some 1,500 M2 Targeting Local Lesions In Genomes populations exist currently. Finally, transformation methods by biolistics and Agrobacterium have been developed, which can be applied for genetic engineering. Root transformation via A. rhizogenes is also possible. Thus, the Phaseomics community has laid a solid foundation towards its ultimate goal, namely the sequencing of the Phaseolus genome. These genomic resources are a much-needed source of additional markers of known map location for marker-assisted selection and the accelerated improvement of common bean cultivars.
Genomics, genetics and breeding of common bean in Africa: A review of tropical legume project
Plant Breeding
Common bean (Phaseolus vulgaris L.) is an important legume crop worldwide. The International Centre for Tropical Agriculture (CIAT) and its national partners in Africa aim to overcome production constraints of common bean and address the food, nutrition needs and market demands through development of multitrait bean varieties. Breeding is guided by principles of market-driven approaches to develop client-demanded varieties. Germplasm accessions from especially two sister species, P. coccineus and P. acutifolius, have been utilized as sources of resistance to major production constraints and interspecific lines deployed. Elucidation of plant mechanisms governing pest and disease resistance, abiotic stress tolerance and grain nutritional quality guides the selection methods used by the breeders. Molecular markers are used to select for resistance to key diseases and insect pests. Efforts have been made to utilize modern genomic tools to increase scale, efficiency, accuracy and speed of breeding. Through gender-responsive participatory variety selection, market-demanded varieties have been released in several African countries. These new bean varieties are a key component of sustainable food systems in the tropics. K E Y W O R D S breeding tools, common bean, demand-led, micronutrient content, production constraints 1 | INTRODUCTION Common bean (Phaseolus vulgaris L.) is grown on about 30 million hectares globally and on 7.6 million ha in Africa annually where it is consumed and traded by more than 100 million households (Buruchara et al., 2011; FAOSTAT, 2014). Being a major staple, common bean contributes to health, food and nutritional security as it is wellendowed with starch, protein, fibre and minerals such as iron, zinc, potassium, selenium, molybdenum and vitamins (thiamine, vitamin B6) and folate. It is an ideal crop for the smallholder farming systems due to its capability to fix N, short maturity period (≤3 months), easily converted to cash to meet urgent household needs, relatively long storage and convenience of handling the harvest and its compatibility with other crops (maize, cassava, banana, etc.), in many low-input production systems. Three East African countries, Kenya, Tanzania and Uganda, are among the global leaders of common bean production (Akibode & Maredia, 2011; FAOSTAT, 2016). The per capita consumption of 40-60 kg/year in Rwanda, Kenya and Uganda is the highest in the world (Beebe, Rao, Blair, & Acosta-Gallegos, 2013; Broughton et al., 2003). A unique partnership model involving CIAT and its research partners, together with effective breeding and seed delivery strategies, have helped to reach millions of beneficiaries with improved bean varieties (Buruchara et al., 2011). There is a notable increase in bean production in most African countries in the
Euphytica, 2015
Common bean is one of the most important legume crops worldwide. Response to selection and success of hybridisation in common bean primarily depends on the nature and magnitude of genetic diversity present in the germplasm used. Germplasm comprising 4274 accessions originating from 58 countries were characterized for 22 phenotypic traits for two years. Genetic diversity for traits such as leaf length (4.5-20.7 cm), leaf width (3.4-17.5 cm), pod length (PL) (3.5-23.5 cm), no of pods/plant (4.2-59.6), seeds/pod (2.1-9.6) and 100-seed weight (SWT) (3.5-96.3 g) was observed in the accessions. Based on multivariate analysis, the entire collection was grouped into 10 genetically diverse clusters irrespective of the origin or place of collection of accessions. First three components obtained through principal component analysis explained 80.44 % of the total variance and it was contributed mainly by PL, pod width (PW), seed length (SL), seed width (SW), pods/plant and SWT. Correlation coefficient of seed weight was positively significant with leaf length, PL, PW, SL and SW while it was negatively correlated with days to flowering, pods/plant and seeds/pod. Regression analysis showed highest direct effect of SW on seed weight followed by SL, and PL. For bean anthracnose, [600 accessions showed resistance under field conditions, however when subjected to screening under artificial conditions against four most prevalent races (03, 515, 598 and 529) of Colletotrichum lindemutianum, we identified 16 accessions which have complete resistance and good agronomic superiority. These accessions may serve as useful genetic material to plant breeders for breeding bean varieties for anthracnose resistance and high yield.
BMC Genomics, 2020
Background Common bean is an important staple crop in the tropics of Africa, Asia and the Americas. Particularly smallholder farmers rely on bean as a source for calories, protein and micronutrients. Drought is a major production constraint for common bean, a situation that will be aggravated with current climate change scenarios. In this context, new tools designed to understand the genetic basis governing the phenotypic responses to abiotic stress are required to improve transfer of desirable traits into cultivated beans. Results A multiparent advanced generation intercross (MAGIC) population of common bean was generated from eight Mesoamerican breeding lines representing the phenotypic and genotypic diversity of the CIAT Mesoamerican breeding program. This population was assessed under drought conditions in two field trials for yield, 100 seed weight, iron and zinc accumulation, phenology and pod harvest index. Transgressive segregation was observed for most of these traits. Yiel...
Frontiers in Plant Science, 2021
Dry bean (Phaseolus vulgaris L.) is an important worldwide legume crop with low to moderate levels of resistance to common bacterial blight (CBB) caused by Xanthomonas axonopodis pv. phaseoli. A total of 852 genotypes (cultivars, preliminary and advanced breeding lines) from the North Dakota State University dry bean breeding program were tested for their effectiveness as populations for genome-wide association studies (GWAS) to identify genomic regions associated with resistance to CBB, to exploit the associated markers for marker-assisted breeding (MAB), and to identify candidate genes. The genotypes were evaluated in a growth chamber for disease resistance at both the unifoliate and trifoliate stages. At the unifoliate stage, 35% of genotypes were resistant, while 25% of genotypes were resistant at the trifoliate stage. Libraries generated from each genotype were sequenced using the Illumina platform. After filtering for sequence quality, read depth, and minor allele frequency, 4...
Agronomic potential of genebank landrace elite accessions for common bean genetic breeding
Scientia Agricola, 2014
Plant breeding effi ciency relies mainly on genetic diversity and selection to release new cultivars. This study aimed to identify landraces with favorable characteristics that can be used as parents of segregating populations in common bean (Phaseolus vulgaris L.) breeding programs. Firstly, ten bean genotypes were selected because they showed promising agronomic performance, and the following seven adaptive traits of four commercial bean cultivars were evaluated: i) plant height; ii) diameter of the stem; iii) height of the insertion of the fi rst pod; iv) pod number per plant; v) grain number per pod; vi) weight of a thousand grains and vii) grain yield. The accessions BAF 07, BAF 44, and BAF 45 are promising in terms of increasing plant height, and accession BAF 01, in terms of reducing plant height. The accession BAF 07 was also the most promising in terms of a plant ideotype that combines higher plant height, maximum height of the insertion of the fi rst pod, and increment in grain yield. Moreover, the selection can be made between and within accessions, because genetic variability is also present within landraces.