Genetic mapping for agronomic traits in a MAGIC population of common bean (Phaseolus vulgaris L.) under drought conditions

Abstract 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. Yield was positively correlated with yield components and pod harvest index (PHI), and negative correlations were found with phenology traits and micromineral contents. Founder haplotypes in the population were identified using Genotyping by Sequencing (GBS). No major population structure was observed in the population. Whole Genome Sequencing (WGS) data from the founder lines was used to impute genotyping data for GWAS. Genetic mapping was carried out with two methods, using association mapping with GWAS, and linkage mapping with haplotype-based interval screening. Thirteen high confidence QTL were identified using both methods and several QTL hotspots were found controlling multiple traits. A major QTL hotspot located on chromosome Pv01 for phenology traits and yield was identified. Further hotspots affecting several traits were observed on chromosomes Pv03 and Pv08. A major QTL for seed Fe content was contributed by MIB778, the founder line with highest micromineral accumulation. Based on imputed WGS data, candidate genes are reported for the identified major QTL, and sequence changes were identified that could cause the phenotypic variation. Conclusions This work demonstrates the importance of this common bean MAGIC population for genetic mapping of agronomic traits, to identify trait associations for molecular breeding tool design and as a new genetic resource for the bean research community.

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Evidence for genotypic differences among elite lines of common bean in the ability to remobilize photosynthate to increase yield under drought

The Journal of Agricultural Science ◽

10.1017/s0021859616000915 ◽

2016 ◽

Vol 155 (6) ◽

pp. 857-875 ◽

Cited By ~ 21

Author(s):

I. M. RAO ◽

S. E. BEEBE ◽

J. POLANIA ◽

M. GRAJALES ◽

C. CAJIAO ◽

...

Keyword(s):

Drought Stress ◽

Grain Yield ◽

Common Bean ◽

Harvest Index ◽

Genotypic Differences ◽

Area Index ◽

Wild Bean ◽

Terminal Drought ◽

Terminal Drought Stress ◽

Pod Harvest Index

SUMMARYCommon bean (Phaseolus vulgaris L.) is the most important food legume for human consumption. Drought stress is the major abiotic stress limitation of bean yields in smallholder farming systems worldwide. The current work aimed to determine the role of enhanced photosynthate mobilization to improve adaptation to intermittent and terminal drought stress and to identify a few key adaptive traits that can be used for developing drought-resistant genotypes. Field studies were conducted over three seasons at Centro Internacional de Agricultura Tropical, Palmira, Colombia to determine genotypic differences in adaptation to intermittent (two seasons) and terminal (one season) drought stress compared with irrigated conditions. A set of 36 genotypes, including 33 common bean, two wild bean and one cowpea were evaluated using a 6 × 6 lattice design under irrigated and rainfed field conditions. Three common bean elite lines (NCB 226, SEN 56, SER 125) were identified with superior levels of adaptation to both intermittent and terminal drought stress conditions. The greater performance of these lines under drought stress was associated with their ability to remobilize photosynthate to increase grain yield based on higher values of harvest index, pod harvest index, leaf area index and canopy biomass. Two wild bean germplasm accessions (G 19902, G 24390) showed very poor adaptation to both types of drought stress. One small-seeded black line (NCB 226) was superior in combining greater values of canopy biomass with greater ability to mobilize photosynthates to grain under both types of drought stress. Two small-seeded red lines (SER 78, SER 125) seem to combine the desirable traits of enhanced mobilization of photosynthates to seed with effective use of water through canopy cooling under terminal drought stress. Pod harvest index showed significant positive association with grain yield under both types of drought stress and this trait can be used by breeders as an additional selection method to grain yield in evaluation of breeding populations for both types of drought stress.

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Genetic Correlation Between Fe and Zn Biofortification and Yield Components in a Common Bean (Phaseolus vulgaris L.)

Frontiers in Plant Science ◽

10.3389/fpls.2021.739033 ◽

2022 ◽

Vol 12 ◽

Author(s):

Santiago Diaz ◽

Jose Polania ◽

Daniel Ariza-Suarez ◽

Cesar Cajiao ◽

Miguel Grajales ◽

...

Keyword(s):

Phaseolus Vulgaris ◽

Common Bean ◽

Yield Components ◽

Harvest Index ◽

Association Studies ◽

Phenotypic Correlation ◽

Human Consumption ◽

Genome Wide Association Studies ◽

New Cultivars ◽

Pod Harvest Index

Common bean (Phaseolus vulgaris L.) is the most important legume for direct human consumption worldwide. It is a rich and relatively inexpensive source of proteins and micronutrients, especially iron and zinc. Bean is a target for biofortification to develop new cultivars with high Fe/Zn levels that help to ameliorate malnutrition mainly in developing countries. A strong negative phenotypic correlation between Fe/Zn concentration and yield is usually reported, posing a significant challenge for breeders. The objective of this study was to investigate the genetic relationship between Fe/Zn. We used Quantitative Trait Loci (QTLs) mapping and Genome-Wide Association Studies (GWAS) analysis in three bi-parental populations that included biofortified parents, identifying genomic regions associated with yield and micromineral accumulation. Significant negative correlations were observed between agronomic traits (pod harvest index, PHI; pod number, PdN; seed number, SdN; 100 seed weight, 100SdW; and seed per pod, Sd/Pd) and micronutrient concentration traits (SdFe and SdZn), especially between pod harvest index (PHI) and SdFe and SdZn. PHI presented a higher correlation with SdN than PdN. Seventy-nine QTLs were identified for the three populations: 14 for SdFe, 12 for SdZn, 13 for PHI, 11 for SdN, 14 for PdN, 6 for 100SdW, and 9 for Sd/Pd. Twenty-three hotspot regions were identified in which several QTLs were co-located, of which 13 hotpots displayed QTL of opposite effect for yield components and Fe/Zn accumulation. In contrast, eight QTLs for SdFe and six QTLs for SdZn were observed that segregated independently of QTL of yield components. The selection of these QTLs will enable enhanced levels of Fe/Zn and will not affect the yield performance of new cultivars focused on biofortification.

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Productive performance of soybean cultivars grown in different plant densities

Ciência Rural ◽

10.1590/0103-8478cr20160928 ◽

2017 ◽

Vol 47 (7) ◽

Cited By ~ 2

Author(s):

Augusto Belchior Marchetti Ribeiro ◽

Adriano Teodoro Bruzi ◽

Alan Mario Zuffo ◽

Everton Vinicius Zambiazzi ◽

Igor Oliveri Soares ◽

...

Keyword(s):

Grain Yield ◽

Plant Height ◽

Harvest Index ◽

Plant Density ◽

Agronomic Traits ◽

Management Practice ◽

Minas Gerais ◽

Index Number ◽

Plant Densities ◽

Pod Harvest Index

ABSTRACT: Plants density in soybean cultivation is an important management practice to achieve high grain yield. In this way, the objective was to evaluate the agronomic traits and grain yield in soybean in different plant densities, in two locations in the south of Minas Gerais. The experimental design was in randomized blocks, arranged in a split plot design, with three replications. Plots were composed of four population densities (300, 400, 500 and 600 thousand plants per hectare) and the subplots were composed of six cultivars (‘BMX Força RR’, ‘CD 250 RR’, ‘FMT 08 - 60.346/1’, ‘NA 5909 RR’, ‘TMG 7161 RR’ and ‘V - TOP RR’) grown in Lavras and Inconfidentes, both in Minas Gerais. At the time of harvest was determined the plant height, lodging, insertion of the first pod, harvest index, number of pods per plant, number of grains, number of grains per pod and yield. Regardless of the soybean cultivar, the plant density of up to 600,000 per ha does not affect grain yield, plant height, lodging, harvest index, and number of grains per pod. The cultivars ‘V-TOP RR’ and ‘BMX FORÇA RR’ showed high grain yield and good agronomic traits in Lavras and Incofidentes.

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Genetic Mapping of Agronomic Traits in Common Bean

Crop Science ◽

10.2135/cropsci2002.5440 ◽

2002 ◽

Vol 42 (2) ◽

pp. 544-556 ◽

Cited By ~ 27

Author(s):

Bunyamin Tar'an ◽

Thomas E. Michaels ◽

K. Peter Pauls

Keyword(s):

Genetic Mapping ◽

Common Bean ◽

Agronomic Traits

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A multi-parent advanced generation inter-cross population for genetic analysis of multiple traits in cowpea (Vigna unguiculata L. Walp.)

10.1101/149476 ◽

2017 ◽

Cited By ~ 3

Author(s):

Bao-Lam Huynh ◽

Jeffrey D. Ehlers ◽

Maria Munoz-Amatriain ◽

Stefano Lonardi ◽

Jansen R. P. Santos ◽

...

Keyword(s):

Genetic Mapping ◽

Vigna Unguiculata ◽

Seed Quality ◽

Agronomic Traits ◽

Recombinant Inbred Lines ◽

Sub Saharan Africa ◽

Yield Potential ◽

Breeding Populations ◽

Advanced Generation ◽

Magic Population

AbstractDevelopment and analysis of Multiparent Advanced Generation Inter-Cross (MAGIC) populations have been conducted with several crop plants to harness the potential for dissecting the genetic structure of traits and improving breeding populations. We developed a first MAGIC population for cowpea (Vigna unguiculata L. Walp.) from eight founder parents which are genetically diverse and carry many abiotic and biotic stress resistance, seed quality and agronomic traits relevant to cowpea improvement in sub-Saharan Africa (SSA) where cowpea is vitally important in the human diet and in local economies. The eight parents were inter-crossed using structured matings to ensure the population would have balanced representation from each of the founder parents, followed by single-seed descent, resulting in 365 F8 recombinant inbred lines (RILs) each carrying a mosaic of genome blocks contributed from all founders. This was confirmed by SNP genotyping with the cowpea Illumina 60K iSelect BeadArray. Following filtering to eliminate duplicates, sister lines and accidental selfing events, a core set of 305 F8 RILs was chosen as the primary population. The F8 lines were on average 99.74% homozygous while also diverse in agronomic traits including flowering time, growth habit, maturity, yield potential and seed characteristics across environments. Trait-associated SNPs were identified for most of the parental traits. Loci with major effects on photoperiod sensitivity and seed size were also verified by genetic mapping in biparental RIL populations. The distribution of recombination frequency varied considerably between chromosomes, with recombination hotspots distributed mostly in the telomeric regions. Due to its broad genetic base, this cowpea MAGIC population promises breakthroughs in genetic gain and high-resolution genetic mapping for gene discovery, enhancement of breeding populations and, for some lines, direct releases as new varieties.

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Drought sensitivity of leaflet growth, biomass accumulation, and resource partitioning predicts yield in common bean

10.1101/736199 ◽

2019 ◽

Author(s):

Amber Hageman ◽

Milan O. Urban ◽

Elizabeth Van Volkenburgh

Keyword(s):

Phaseolus Vulgaris ◽

Common Bean ◽

Biomass Production ◽

Seed Yield ◽

Growth Rates ◽

Resource Partitioning ◽

Harvest Index ◽

Biomass Accumulation ◽

Pod Growth ◽

Pod Harvest Index

ABSTRACTWhile drought limits yield largely by its impact on photosynthesis and therefore biomass accumulation, biomass is not the strongest predictor of yield under drought. Instead, resource partitioning efficiency, measured by how much total pod weight is contained in seeds at maturity (Pod Harvest Index), is the stronger correlate in Phaseolus vulgaris. Using 20 field-grown genotypes, we expanded on this finding by pairing yield and resource partitioning data with growth rates of leaflets and pods. We hypothesized that genotypes which decreased partitioning and yield most under drought would also have strongest decreases in growth rates. We found that while neither leaflet nor pod growth rates correlated with seed yield or partitioning, impacts to leaflet growth rates under drought correlate with impacts to yield and partitioning. As expected, biomass production correlated with yield, yet correlations between the decreases to these two traits under drought were even stronger. This suggests that while biomass contributes to yield, biomass sensitivity to drought is a stronger predictor. Lastly, under drought, genotypes may achieve similar canopy biomass yet different yields, which can be explained by higher or lower partitioning efficiencies. Our findings suggest that inherent sensitivity to drought may be used as a predictor of yield.HIGHLIGHTIn common bean, higher biomass accumulation under drought alone does not guarantee higher yield, as maintenance of higher growth rates and partitioning processes act as an additional requirement.

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Genetic Mapping of Agronomic Traits in Common Bean

Crop Science ◽

10.2135/cropsci2002.0544 ◽

2002 ◽

Vol 42 (2) ◽

pp. 544 ◽

Cited By ~ 46

Author(s):

Bunyamin Tar'an ◽

Thomas E. Michaels ◽

K. Peter Pauls

Keyword(s):

Genetic Mapping ◽

Common Bean ◽

Agronomic Traits

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Performance Evaluation of Grain Yield and Yield Related Traits in Common bean Genotypes at Yabello and Abaya, Southern Ethiopia

Journal of Aridland Agriculture ◽

10.25081/jaa.2017.v3.3365 ◽

1970 ◽

Vol 3 ◽

pp. 28-34

Author(s):

Ejigu Ejara, Wassu Mohammed, Berhanu Amsalu ◽

Zinash Misgana, Mulatu Gabisa, Ganane Tasama

Keyword(s):

Grain Yield ◽

Common Bean ◽

Agronomic Traits ◽

Southern Ethiopia ◽

Design Data ◽

Nutrition Security ◽

Lattice Design ◽

Food And Nutrition ◽

Borana Zone ◽

Home Consumption

Common bean is among the major crops grown in southern Ethiopia including Borana zone where the majority of the farmers are Agro-pastoralist and produce the crop mainly for home consumption. The area has potential to the production of common bean for food and nutrition security as well as export commodity. However, scarcity of varieties that fit to the environment is one of the major constraints of production. Therefore, this experiment was conducted to evaluate 36 common bean genotypes including seven released varieties to evaluate performance of genotypes for yield and agronomic traits. The field experiment was conducted in 2015 at two locations (Abaya and Yabello) and genotypes were planted in triple lattice design. Data were collected on yield and important agronomic traits. Analysis of variance computed for individual locations and combined analysis over locations revealed significant variations among genotypes for all traits. Moreover, 16.67% of the genotypes had mean grain yield greater than the best performing released variety across locations and the genotypes showed a grain yield as high as 3.25 tons ha-1. Based on results of this study it is recommended to test the high yielding and early maturing genotypes at many locations to develop preferred varieties across many locations.

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Impact assessment of common bean availability in Brazil under climate change scenarios

Agricultural Systems ◽

10.1016/j.agsy.2021.103174 ◽

2021 ◽

Vol 191 ◽

pp. 103174

Author(s):

Luís A.S. Antolin ◽

Alexandre B. Heinemann ◽

Fábio R. Marin

Keyword(s):

Climate Change ◽

Impact Assessment ◽

Common Bean ◽

Climate Change Scenarios

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Influence of Organic and Inorganic Fertilizers on Coriander (Coriandrum sativum L.) Agronomic Traits, Essential Oil and Components under Semi-Arid Climate

Agronomy ◽

10.3390/agronomy11071427 ◽

2021 ◽

Vol 11 (7) ◽

pp. 1427

Author(s):

Gulen Ozyazici

Keyword(s):

Essential Oil ◽

Seed Yield ◽

Harvest Index ◽

Agronomic Traits ◽

Climatic Conditions ◽

Coriandrum Sativum ◽

Inorganic Fertilizers ◽

Yield And Quality ◽

Biological Yield

Environmental contamination and the excessive use of inorganic fertilizers resulting in stagnant yields of field crops which necessitate the utilization of combined fertilization approach under changing climatic conditions. Current study was aimed to clarify the influence of several fertilizer sources (chemical, organic, organomineral fertilizers) on yield and quality of coriander (Coriandrum sativum L.). The results revealed that the fertilizer sources significantly affected the yield of coriander cultivars. The absence of “Year x Variety x Fertilizer Type” interactions for any of the noted parameters signaled that the detected “Variety x Fertilizer Type” interactions were constant regardless of the year factor. The recorded values of traits according to fertilizer sources different for the plant height from 61.85 to 69.67 cm, number of branches from 5.98 to 7.71 (piece/plant), number of umbels per the main umbel from 5.62 to 7.18 pieces, seed yield from 1.06 to 1.66 t/ha, the biological yield from 4.29 to 5.70 t ha−1, harvest index from 25.29 to 29.41%, essential oil ratio from 0.29 to 0.33%, and essential oil yield from 3.1 to 5.6 L ha−1. Erbaa variety was observed to be superior over the rest of the varieties producing the maximum values of 6.5 L ha−1 of essential oil, 0.36% essential oil content, 30.9% harvest index, 1.81 t/ha seed yield, and 5.9 t ha−1 biological yield with the treatment of chemical fertilizers.

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