Multilocation dataset on seed Fe and Zn contents of bean (Phaseolus vulgaris L.) genotypes grown in Tanzania.
ABSTRACT: There are over a hundred genotypes of Phaseolus vulgaris L. grown and consumed in Tanzania. Currently, identification of bean genotypes containing high seed iron and zinc contents has been the focus globally for common bean iron and zinc biofortification. Diversity in seed iron and zinc contents were investigated in 99 bean genotypes grown in Tanzania to identify high seed iron and zinc-containing genotypes for use in iron and zinc biofortification. Flour obtained by grinding seeds of each bean genotypes was used in the determination of iron and zinc concentrations. Data were subjected to analysis of variance (ANOVA) to determine significant differences among common bean genotypes in terms of seed iron and zinc contents. Additive main effects and multiplicative interaction (AMMI) and genotype plus genotype by environment interaction (GGE) were conducted to determine stability and adaptation across sites (TARI-Selian, SUA, and TARI-Uyole) of bean genotypes in terms of seed iron and zinc contents. Data in this data article show that some landraces had high seed iron and zinc contents compared to release varieties thus can be used for iron and zinc genetic biofortification in common beans breeding programs. For more explanation of the data presented in this data article, please follow the related research article "Environmental and genotypes influence on seed iron and zinc levels of landraces and improved varieties of common bean (Phaseolus vulgaris L.) in Tanzania" .
Project description:Common beans (Phaseolus vulgaris L.), like many legumes, are rich in iron, zinc, and certain other microelements that are generally found to be in low concentrations in cereals, other seed crops, and root or tubers and therefore are good candidates for biofortification. But a quandary exists in common bean biofortification: namely that the distribution of iron has been found to be variable between the principal parts of seed; namely the cotyledonary tissue, embryo axis and seed coat. The seed coat represents ten or more percent of the seed weight and must be considered specifically as it accumulates much of the anti-nutrients such as tannins that effect mineral bioavailability. Meanwhile the cotyledons accumulate starch and phosphorus in the form of phytates. The goal of this study was to evaluate a population of progeny derived from an advanced backcross of a wild bean and a cultivated Andean bean for seed coat versus cotyledonary minerals to identify variability and predict inheritance of the minerals. We used wild common beans because of their higher seed mineral concentration compared to cultivars and greater proportion of seed coat to total seed weight. Results showed the most important gene for seed coat iron was on linkage group B04 but also identified other QTL for seed coat and cotyledonary iron and zinc on other linkage groups, including B11 which has been important in studies of whole seed. The importance of these results in terms of physiology, candidate genes and plant breeding are discussed.
Project description:Mineral deficiencies represent a global challenge that needs to be urgently addressed. An adequate intake of iron and zinc results in a balanced diet that reduces chances of impairment of many metabolic processes that can lead to clinical consequences. In plants, bioavailability of such nutrients is reduced by presence of compounds such as phytic acid, that can chelate minerals and reduce their absorption. Biofortification of common bean (Phaseolus vulgaris L.) represents an important strategy to reduce mineral deficiencies, especially in areas of the world where this crop plays a key role in the diet. In this study, a panel of diversity encompassing 192 homozygous genotypes, was screened for iron, zinc and phytate seed content. Results indicate a broad variation of these traits and allowed the identification of accessions reasonably carrying favourable trait combinations. A significant association between zinc seed content and some molecular SNP markers co-located on the common bean Pv01 chromosome was detected by means of genome-wide association analysis. The gene Phvul001G233500, encoding for an E3 ubiquitin-protein ligase, is proposed to explain detected associations. This result represents a preliminary evidence that can foster future research aiming at understanding the genetic mechanisms behind zinc accumulation in beans.
Project description:Dry bean (Phaseolus vulgaris L.) seeds are a rich source of dietary zinc, especially for people consuming plant-based diets. Within P. vulgaris there is at least two-fold variation in seed Zn concentration. Genetic studies have revealed seed Zn differences to be controlled by a single gene in two closely related navy bean genotypes, Albion and Voyager. In this study, these two genotypes were grown under controlled fertilization conditions and the Zn concentration of various plant parts was determined. The two genotypes had similar levels of Zn in their leaves and pods but Voyager had 52% more Zn in its seeds than Albion. RNA was sequenced from developing pods of both genotypes. Transcriptome analysis of these genotypes identified 27,198 genes in the developing bean pods, representing 86% of the genes in the P. vulgaris genome (v 1.0 DOE-JGI and USDA-NIFA). Expression was detected in 18,438 genes. A relatively small number of genes (381) were differentially expressed between Albion and Voyager. Differentially expressed genes included three genes potentially involved in Zn transport, including zinc-regulated transporter, iron regulated transporter like (ZIP), zinc-induced facilitator (ZIF) and heavy metal associated (HMA) family genes. In addition 12,118 SNPs were identified between the two genotypes. Of the gene families related to Zn and/or Fe transport, eleven genes were found to contain SNPs between Albion and Voyager.
Project description:Dry bean (Phaseolus vulgaris L.) seeds are a rich source of dietary zinc, especially for people consuming plant-based diets. Within P. vulgaris there is at least two-fold variation in seed Zn concentration. Genetic studies have revealed seed Zn differences to be controlled by a single gene in two closely related navy bean genotypes, Albion and Voyager. In this study, these two genotypes were grown under controlled fertilization conditions and the Zn concentration of various plant parts were determined. The two genotypes had similar levels of Zn in their leaves and pods but Voyager had 52% more Zn in its seeds than Albion. RNA was sequence from developing pods of both genotypes. Transcriptome analysis of these genotypes identified 27,198 genes in the developing bean pods, representing 86% of the genes in the P. vulgaris genome (v 1.0 DOE-JGI and USDA-NIFA). Expression was detected in 18,438 genes. A relatively small number of genes (381) were differentially expressed between Albion and Voyager. Differentially expressed genes included three genes potentially involved in Zn transport, including zinc-regulated transporter, iron regulated transporter like (ZIP), zinc-induced facilitator (ZIF) and heavy metal associated (HMA) family genes. In addition 12,118 SNPs were identified between the two genotypes. Of the gene families related to Zn and/or Fe transport, eleven genes were found to contain SNPs between Albion and Voyager. Overall design: Transcriptome of developing pods of two contrasting common bean genotypes in zinc concentration generated by deep sequencing using Illumina Genome Analyzer II
Project description:Common bean (Phaseolus vulgaris L.) is an important source of dietary protein and minerals worldwide. Genes conditioning variability for mineral contents are not clearly understood. Our ultimate goal is to identify genes conditioning genetic variation for Zn and Fe content. To establish mapping populations for this objective, we tested mineral content of 29 common bean genotypes. Chemical analyses revealed significant genetic variability for seed Zn and Fe contents among the genotypes. Genetic diversity was evaluated with 49 primer pairs, of which 23 were simple sequence repeats (SSR), 16 were developed from tentative consensus (TC) sequences, and 10 were generated from common bean NBS-LRR gene sequences. The discriminatory ability of molecular markers for identifying allelic variation among genotypes was estimated by polymorphism information content (PIC) and the genetic diversity was measured from genetic similarities between genotypes. Primers developed from NBS-LRR gene sequences were highly polymorphic in both PIC values and number of alleles (0.82 and 5.3), followed by SSRs (0.56 and 3.0), and markers developed from TC (0.39 and 2.0). genetic similarity values between genotypes ranged from 14.0 (JaloEEP558 and DOR364) to 91.4 (MIB152 and MIB465). Cluster analysis clearly discriminated the genotypes into Mesoamerican and Andean gene pools. Common bean genotypes were selected to include in crossing to enhance seed Zn and Fe content based on genetic diversity and seed mineral contents of the genotypes.
Project description:Common bean (Phaseolus vulgaris) is an annual grain legume that was domesticated in Mesoamerica (Central America) and the Andes. It is currently grown widely also on other continents including Africa. We surveyed seedborne viruses in new common bean varieties introduced to Nicaragua (Central America) and in landraces and improved varieties grown in Tanzania (eastern Africa). Bean seeds, harvested from Nicaragua and Tanzania, were grown in insect-controlled greenhouse or screenhouse, respectively, to obtain leaf material for virus testing. Equal amounts of total RNA from different samples were pooled (30-36 samples per pool), and small RNAs were deep-sequenced (Illumina). Assembly of the reads (21-24 nt) to contiguous sequences and searches for homologous viral sequences in databases revealed Phaseolus vulgaris endornavirus 1 (PvEV-1) and PvEV-2 in the bean varieties in Nicaragua and Tanzania. These viruses are not known to cause symptoms in common bean and are considered non-pathogenic. The small-RNA reads from each pool of samples were mapped to the previously characterized complete PvEV-1 and PvEV-2 sequences (genome lengths ca. 14 kb and 15 kb, respectively). Coverage of the viral genomes was 87.9-99.9%, depending on the pool. Coverage per nucleotide ranged from 5 to 471, confirming virus identification. PvEV-1 and PvEV-2 are known to occur in Phaseolus spp. in Central America, but there is little previous information about their occurrence in Nicaragua, and no information about occurrence in Africa. Aside from Cowpea mild mosaic virus detected in bean plants grown from been seeds harvested from one region in Tanzania, no other pathogenic seedborne viruses were detected. The low incidence of infections caused by pathogenic viruses transmitted via bean seeds may be attributable to new, virus-resistant CB varieties released by breeding programs in Nicaragua and Tanzania.
Project description:Common bean (Phaseolus vulgaris) was domesticated ?8000 years ago in the Americas and today is a staple food worldwide. Besides caloric intake, common bean is also an important source of protein and micronutrients and it is widely appreciated in developing countries for their affordability (compared to animal protein) and its long storage life. As a legume, common bean also has the economic and environmental benefit of associating with nitrogen-fixing bacteria, thus reducing the use of synthetic fertilizers, which is key for sustainable agriculture. Despite significant advances in the plant nutrition field, the mechanisms underlying the adaptation of common bean to low nutrient input remains largely unknown. The recent release of the common bean genome offers, for the first time, the possibility of applying techniques and approaches that have been exclusive to model plants to study the adaptive responses of common bean to challenging environments. In this review, we discuss the hallmarks of common bean domestication and subsequent distribution around the globe. We also discuss recent advances in phosphate, iron, and zinc homeostasis, as these nutrients often limit plant growth, development, and yield. In addition, iron and zinc are major targets of crop biofortification to improve human nutrition. Developing common bean varieties able to thrive under nutrient limiting conditions will have a major impact on human nutrition, particularly in countries where dry beans are the main source of carbohydrates, protein and minerals.
Project description:Biofortification is an effective method to improve the nutritional content of crops and nutritional intake. Breeding for higher micronutrient mineral content in beans is correlated with an increase in phytic acid, a main inhibitor of mineral absorption in humans. Low phytic acid (lpa) beans have a 90% lower phytic acid content compared to conventional beans. This is the first study to investigate mineral and total phytic acid retention after preparing common household recipes from conventional, biofortified and lpa beans. Mineral retention was determined for two conventional, three biofortified and two lpa bean genotypes. Treatments included soaking, boiling (boiled beans) and refrying (bean paste). The average true retention of iron after boiling was 77.2-91.3%; for zinc 41.2-84.0%; and for phytic acid 49.9-85.9%. Soaking led to a significant decrease in zinc and total phytic acid after boiling and refrying, whereas for iron no significant differences were found. lpa beans did not exhibit a consistent pattern of difference in iron and phytic acid retention compared to the other groups of beans. However, lpa beans had a significantly lower retention of zinc compared to conventional and biofortified varieties (p < 0.05). More research is needed to understand the underlying factors responsible for the differences in retention between the groups of beans, especially the low retention of zinc. Combining the lpa and biofortification traits could further improve the nutritional benefits of biofortified beans, by decreasing the phytic acid:iron and zinc ratio in beans.
Project description:Micronutrient deficiencies are of major concern in human health and plant metabolism. Iron (Fe), zinc (Zn), iodine (I), selenium (Se) are regarded as micronutrients having major impact on human health. More than 50% of populations mainly from developing countries are suffering from one or the other micronutrient malnutrition. Ensuring adequate supply of these micronutrients through diet consisting of staple foods, such as common bean (Phaseolus vulgaris L.) is must. Here, we evaluated common bean genotypes that were collected from various regions of Jammu and Kashmir, India for Fe, Zn and protein contents and used SSRs to identify the markers associated with these traits. We found significant variation among genotypes for Fe, Zn and protein contents. Genotype R2 was having 7.22 mg 100 g-1 of Fe content, genotype K15 with 1.93 mg 100 g-1 of Zn content and genotype KS6 with 31.6% of protein content. Diversity study was done using both cluster and structure based approach. Further, association mapping analysis using General Linear Method (GLM) approach was done to identify SSRs associated with accumulation of Fe, Zn and protein. 13 SSRs were identified that significantly (p < 0.05) showed association with Fe, Zn and protein contents in common bean. The markers associated with Fe were located on chromosome no. 2, 5, 6, 7, 9 and 10, markers associated with Zn were located on chromosome no. 1, 3, 5, 7 and 10 whereas only one marker located on chromosome no. 4 was found associated with protein content. These findings will provide potential opportunity to improve Fe and Zn concentrations in common bean, through molecular breeding.
Project description:Antioxidants play an important role in animal and plant life owing to their involvement in complex metabolic and signaling mechanisms, hence uncovering the genetic basis associated with antioxidant activity is very important for the development of improved varieties. Here, a total of 182 common bean (Phaseolus vulgaris) landraces and six commercial cultivars collected from 19 provinces of Turkey were evaluated for seed antioxidant activity under four environments and two locations. Antioxidant activity was measured using ABTS radical scavenging capacity and mean antioxidant activity in common bean landraces was 20.03 µmol TE/g. Analysis of variance reflected that genotype by environment interaction was statistically non-significant and heritability analysis showed higher heritability of antioxidant activity. Variations in seed color were observed, and a higher antioxidant activity was present in seeds having colored seed as compared to those having white seeds. A negative correlation was found between white-colored seeds and antioxidant activity. A total of 7900 DArTseq markers were used to explore the population structure that grouped the studied germplasm into two sub-populations on the basis of their geographical origins and trolox equivalent antioxidant capacity contents. Mean linkage disequilibrium (LD) was 54%, and mean LD decay was 1.15 Mb. Mixed linear model i.e., the Q + K model demonstrated that four DArTseq markers had significant association (p < 0.01) for antioxidant activity. Three of these markers were present on chromosome Pv07, while the fourth marker was located on chromosome Pv03. Among the identified markers, DArT-3369938 marker showed maximum (14.61%) variation. A total of four putative candidate genes were predicted from sequences reflecting homology to identified DArTseq markers. This is a pioneering study involving the identification of association for antioxidant activity in common bean seeds. We envisage that this study will be very helpful for global common bean breeding community in order to develop cultivars with higher antioxidant activity.