Genomics of Phaseolus Beans, a Major Source of Dietary Protein and Micronutrients in the Tropics (original) (raw)
Related papers
Beans (Phaseolus spp.) – model food legumes
Plant and Soil, 2003
Globally, 800 million people are malnourished. Heavily subsidised farmers in rich countries produce sufficient surplus food to feed the hungry, but not at a price the poor can afford. Even donating the rich world's surplus to the poor would not solve the problem. Most poor people earn their living from agriculture, so a deluge of free food would destroy their livelihoods. Thus, the only answer to world hunger is to safeguard and improve the productivity of farmers in poor countries. Diets of subsistence level farmers in Africa and Latin America often contain sufficient carbohydrates (through cassava, corn/maize, rice, wheat, etc.), but are poor in proteins. Dietary proteins can take the form of scarce animal products (eggs, milk, meat, etc.), but are usually derived from legumes (plants of the bean and pea family). Legumes are vital in agriculture as they form associations with bacteria that 'fix-nitrogen' from the air. Effectively this amounts to internal fertilisation and is the main reason that legumes are richer in proteins than all other plants. Thousands of legume species exist but more common beans (Phaseolus vulgaris L.) are eaten than any other. In some countries such as Mexico and Brazil, beans are the primary source of protein in human diets. As half the grain legumes consumed worldwide are common beans, they represent the species of choice for the study of grain legume nutrition. Unfortunately, the yields of common beans are low even by the standards of legumes, and the quality of their seed proteins is sub-optimal. Most probably this results from millennia of selection for stable rather than high yield, and as such, is a problem that can be redressed by modern genetic techniques. We have formed an international consortium called 'Phaseomics' to establish the necessary framework of knowledge and materials that will result in disease-resistant, stress-tolerant, high-quality protein and high-yielding beans. Phaseomics will be instrumental in improving living conditions in deprived regions of Africa and the Americas. It will contribute to social equity and sustainable development and enhance inter-and intra-cultural understanding, knowledge and relationships. A major goal of Phaseomics is to generate new common bean varieties that are not only suitable for but also desired by the local farmer and consumer communities. Therefore, the socioeconomic dimension of improved bean production and the analysis of factors influencing the acceptance of novel varieties will be an integral part of the proposed research (see Figure 1). Here, we give an overview of the economic and nutritional importance of common beans as a food crop. Priorities and targets of current breeding programmes are outlined, along with ongoing efforts in genomics. Recommendations for an international coordinated effort to join knowledge, facilities and expertise in a variety of scientific undertakings that will contribute to the overall goal of better beans are given. To be rapid and effective, plant breeding programmes (i.e., those that involve crossing two different 'parents') rely heavily on molecular 'markers'. These genetic landmarks are used to position
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
Molecular Breeding
Common bean (Phaseolus vulgaris L.), one of the most important grain legume crops for direct human consumption, faces many challenges as a crop. Domesticated from wild relatives that inhabit a relatively narrow ecological niche, common bean faces a wide range of biotic and abiotic constraints within its diverse agroecological settings. Biotic stresses impacting common bean include numerous bacterial, fungal, and viral diseases and various insect and nematode pests, and abiotic stresses include drought, heat, cold, and soil nutrient deficiencies or toxicities. Breeding is often local, focusing on improvements in responses to biotic and abiotic stresses that are particular challenges in certain locations and needing to respond to conditions such as day-length regimes. This review describes the major breeding objectives for common bean, followed by a description of major genetic and genomic resources, and an overview of current and prospective marker-assisted methods in common bean breeding. Improvements over traditional breeding methods in CB can result from the use of different approaches. Several important germplasm collections have been densely genotyped, and relatively inexpensive SNP genotyping platforms enable implementation of genomic selection and related markerassisted breeding approaches. Also important are sociological insights related to demand-led breeding, which considers local value chains, from farmers to traders to retailers and consumers.
Genetic Resources and Crop Evolution, 2022
Common bean (Phaseolus vulgaris L.) is a nutrient-rich food, but its long cooking times hinder its wider utilization. The Yellow Bean Collection (YBC) was assembled with 295 genotypes from global sources to assess the genetic and phenotypic diversity for end-use quality traits in yellow beans. The panel was genotyped with over 2,000 SNPs identified via Genotyping-By-Sequencing (GBS). Through population structure analyses with the GBS markers, the YBC was determined to be 69% Andean, 26% Middle American, and 5% admixture. The YBC was grown in two major bean production regions in the U.S., Michigan (MI) and Nebraska (NE) over two years. The genotypes exhibited a wide diversity in days to flower, seed weight, water uptake, and cooking time. The cooking times of the YBC ranged from 17–123 min. The cooking time were longer and varied more widely in NE with many more genotypes exhibiting hardshell than in MI. Fast-cooking genotypes were identified with various yellow colors; 20 genotypes ...
Diversity of Common Bean (Phaseolus vulgaris L.) Landraces and the Nutritional Value of their Grains
Grain Legumes, 2016
Grain legumes are considered major sources of dietary proteins, calories, certain minerals and vitamins, and they are the most widely cultivated and consumed crops worldwide. Among them are the common beans, whose major production volumes came from landraces cultivated in traditional farming systems. The objective of this study was to evaluate the phenotypic diversity of a set of common bean landraces from Mexico based on the agromorphological traits and nutritional composition of the grain in the context of traditional farming systems. Different field and laboratory data were collected and complemented with secondary information published in refereed journals and research reports. The results showed that there are significant differences in the morphological and physiological traits of the plant, pod and grain among groups of common bean landraces of different geographic origins, which were associated with different indigenous groups. Similar patterns were observed in the contents of anthocyanins, polyphenols, flavoinds and minerals as well as antioxidant activity. In the evaluated population groups in each region, there are outstanding populations in terms of agromorphological traits and the nutritional value of the grain that can enable a participatory breeding initiative guided by regional objectives. Some populations from Sierra Norte, Oaxaca, presented higher values in Zn and Fe, and populations from Estado de Mexico exhibited high polyphenol and flavonoid values but stable agronomic behaviour.
Genetic variation in common bean (Phaseolus vulgaris L.) using seed protein markers
Acta Universitatis Sapientiae, Agriculture and Environment
The genetic diversity of common bean accessions were assessed using seed storage protein markers. At regional level, accessions from the two major growing regions showed the highest level of gene diversity (H = 0.322, I = 0.485, and H = 0.312, I = 0.473), which can be exploited for the future improvement of the crop. Based on phaseolin, the major storage protein in common bean, the majority of the accessions (86%) were grouped under Mesoamerican gene pool. Seed proteins were also used to differentiate various Phaseolus species, indicating the usefulness of seed storage proteins in species identification in this genus.
Tropical Plant …, 2008
Common bean (Phaseolus vulgaris L.) is a legume that is an important source of dietary protein in developing countries throughout the world. Utilizing the G19833 BAC library for P. vulgaris from Clemson University, 89,017 BAC-end sequences were generated giving 62,588,675 base pairs of genomic sequence covering approximately 9.54% of the genome. Analysis of these sequences in combination with 1,404 shotgun sequences from the cultivar Bat7 revealed that approximately 49.2% of the genome contains repetitive sequence and 29.3% is genic. Compared to other legume BAC-end sequencing projects, it appears that P. vulgaris has higher predicted levels of repetitive sequence, but this may be due to a more intense identification strategy combining both similarity-based matches as well as de novo identification of repeats. In addition, fingerprints for 41,717 BACs were obtained and assembled into a draft physical map consisting of 1,183 clone contigs and 6,385 singletons with ~9x coverage of the genome.
Frontiers in plant science, 2016
A series of genetically related lines of common bean (Phaseolus vulgaris L.) integrate a progressive deficiency in major storage proteins, the 7S globulin phaseolin and lectins. SARC1 integrates a lectin-like protein, arcelin-1 from a wild common bean accession. SMARC1N-PN1 is deficient in major lectins, including erythroagglutinating phytohemagglutinin (PHA-E) but not α-amylase inhibitor, and incorporates also a deficiency in phaseolin. SMARC1-PN1 is intermediate and shares the phaseolin deficiency. Sanilac is the parental background. To understand the genomic basis for variations in protein profiles previously determined by proteomics, the genotypes were submitted to short-fragment genome sequencing using an Illumina HiSeq 2000/2500 platform. Reads were aligned to reference sequences and subjected to de novo assembly. The results of the analyses identified polymorphisms responsible for the lack of specific storage proteins, as well as those associated with large differences in sto...
Current State and Perspectives in Population Genomics of the Common Bean
Plants
Population genomics integrates advances in sequencing technologies, bioinformatics tools, statistical methods and software into research on evolutionary and population genetics. Its application has provided novel approaches that have significantly advanced our understanding of new and long-standing questions in evolutionary processes. This has allowed the disentangling of locus-specific effects from genome-wide effects and has shed light on the genomic basis of fitness, local adaptation and phenotypes. “-Omics” tools have provided a comprehensive genome-wide view of the action of evolution. The specific features of the Phaseolus genus have made it a unique example for the study of crop evolution. The well-documented history of multiple domestications in Phaseolus vulgaris L. (common bean) and its further adaptation to different environments have provided the opportunity to investigate evolutionary issues, such as convergent evolution in the same species across different domesticatio...
Variation in protein and amino acids content among landraces of common bean (Phaseolus vulgaris L.)
Emirates Journal of Food and Agriculture, 2020
Native bean populations (Phaseolus vulgaris L.) provide bioactive and nutrient compounds; however, their amino acid profiles are unknown. Therefore, the aim of this study is to evaluate the protein content and amino acid profile of 46 native bean populations cultivated by small farmers in Oaxaca, Mexico, and compare them with that of commercial beans. Through high-performance liquid chromatography (HPLC), 16 amino acids were identified and quantified in all samples. The region of origin influenced the concentrations of amino acids. The Santa Lucia Miahuatlan populations stood out for their high content of isoleucine, threonine, methionine, arginine, serine, alanine, tyrosine, and cysteine. Amino acid content showed high variability among the populations; accessions labeled as FSLM22, FSLM27, FSLM28, and FSLM32 were enriched in aliphatic, hydroxylated, aromatic, acidic, and basic amino acids, while the FSLM14, FSLM17, and FSLM18 populations had the highest concentrations of sulfur am...