Genome‐Wide Association Study of Agronomic Traits in Common Bean

Kamfwa, Kelvin; Cichy, Karen A.

doi:10.3835/plantgenome2014.09.0059

Cited by 90 publications

(134 citation statements)

References 66 publications

(89 reference statements)

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“…This QTL spanned 59.5 to 73.2 cM, with a peak region at 70.0 cM near marker ss715639424 (40.16 Mb). A subsequent study reported significant SNP association for SY on Pv03 associated with marker ss715648538 at 38.27 Mb in Andean bean diversity panel grown under low-N conditions in Michigan (Kamfwa et al, 2015). This was consistent with several previous studies that reported QTL for yield on Pv03 (Wright and Kelly, 2011;Checa and Blair, 2012;Mukeshimana et al, 2014;Hoyos-Villegas et al, 2015;Kamfwa et al, 2015;Heilig et al, 2017).…”

Section: Seed Yield Per Plantsupporting

confidence: 88%

“…SY3.3 PR had a LOD of 3.45 and additive allelic effect of 2.38 g, explaining 9.7% of variation in SY under DS. Interestingly, the significant marker ss715648538 was in strong LD with markers within SY3.3 SC interval, implying that the gene(s) underlying the QTL for seed yield reported in the two studies were the same (Mukeshimana et al, 2014;Kamfwa et al, 2015;Kelly, 2018). The QTL YLD3.1 CG linked to marker BM172 and YLD3.2 CG near marker BM98 for yield were reported in Popayán using an ICA Cerinza ´ G 24404 population .…”

Section: Seed Yield Per Plantmentioning

confidence: 94%

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Identification of QTL Associated with Drought Tolerance in Andean Common Bean

2019

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Drought stress is becoming one of the most important abiotic factors limiting productivity of common bean (Phaseolus vulgaris L.) globally. The objective of this study was to conduct a quantitative trait loci (QTL) analysis of drought tolerance in a recombinant inbred line (RIL) mapping population genotyped using single nucleotide polymorphism (SNP) markers. The RIL population was developed by crossing Portillo × Red Hawk, two Andean bean genotypes contrasting in reaction to drought stress and evaluated at two locations in Uganda for two seasons under drought stress (DS) and non‐stress (NS) conditions. Eighteen significant QTL signals were identified for phenology, yield component and partitioning traits on chromosomes Pv01, Pv02, Pv03, Pv04, Pv06, and Pv11 under DS and NS conditions. Quantitative trait loci for seed yield per plant (SY) were detected on Pv01, Pv02, Pv03, Pv04, and Pv06 under DS conditions. Colocalized QTL signals for pod weight per plant and SY were identified under DS on Pv01 (45.15 Mb) and on Pv02 (0.12 Mb), for phenology and SY on Pv03 near marker ss715639424 (40.16 Mb), and for SY and harvest index on Pv06 (17.92 Mb). Two candidate genes related to flowering were identified within a 35‐kb region from the ss715639424 marker on Pv03. Gene Phvul.003G189100 (30.3 kb) encodes “AGAMOUS‐LIKE 65 (AGL65),” which is essential for pollen development, and gene Phvul.003G189300 (17.9 kb) encodes “CYCLING DOF FACTOR 3 (CDF3)” that regulates flowering time. The same SY QTL, SY3.3PR on Pv03, was previously detected in Mesoamerican germplasm and could be used through marker‐assisted breeding to improve SY of Andean beans grown under DS.

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Section: Seed Yield Per Plantsupporting

confidence: 88%

Section: Seed Yield Per Plantmentioning

confidence: 94%

Identification of QTL Associated with Drought Tolerance in Andean Common Bean

2019

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“…The highest yields were obtained in 2008 when white mold incidence was lowest (20%), largely as a result of weather conditions. Three SNPs within the yield QTL interval on Pv03 identified in the current study were in strong linkage disequilibrium (R 2 = 1) with the most significant SNP for yield in the previous genome-wide association study of the Andean diversity panel (Kamfwa et al, 2015). One hundred-seed weight was relatively constant over years, ranging from 33.6 to 37.6 g, and the lowest seed weight corresponded with the low-yielding year of 2010.…”

Section: Yield and One Hundred-seed Weightsupporting

confidence: 48%

“…The confirmation of yet another QTL for flowering on Pv01 in a distinct genetic population suggests that it may be associated with the phyA gene that codes for photoreceptor pigment phytochrome A in Arabidopsis thaliana (L.) Heynh. The photoperiod Ppd gene on Pv01 in bean is another likely target despite the fact that both parents in this study were adapted to temperate production regions unlike the Andean diversity panel, in which prior QTL were detected among lines differing in photo period sensitivity (Kamfwa et al, 2015). The photoperiod Ppd gene on Pv01 in bean is another likely target despite the fact that both parents in this study were adapted to temperate production regions unlike the Andean diversity panel, in which prior QTL were detected among lines differing in photo period sensitivity (Kamfwa et al, 2015).…”

Section: Days To Flower and Maturitymentioning

confidence: 95%

“…The major QTL, DF1.1, associated with days to flower on Pv01 has been identified in a number of prior studies (Blair et al, 2006;Kamfwa et al, 2015;Koinange et al, 1996;Mukeshimana et al, 2014;Pérez-Vega et al, 2010). that was first reported in common bean by Kamfwa et al (2015). that was first reported in common bean by Kamfwa et al (2015).…”

Section: Days To Flower and Maturitymentioning

confidence: 99%

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Quantitative Trait Loci Analysis of White Mold Avoidance in Pinto Bean

et al. 2015

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White mold is a major disease of common bean (Phaseolus vulgaris L.) grown in temperate production areas. The objective of this study was to use single nucleotide polymorphism (SNP) markers from the BARCBean6K_3 BeadChip to identify quantitative trait loci (QTL) associated with traits related to white mold resistance in common bean. A recombinant inbred line (RIL) population from a cross of disease‐tolerant pinto line AN‐37 and disease‐susceptible line P02630 was evaluated in Michigan for 4 yr under white mold pressure. Traits evaluated included disease incidence, the numbers of days to flower and to maturity, canopy height, lodging, seed yield, and 100‐seed weight. A linkage map of the RIL population spanning 1499 cM was constructed using 447 SNP markers. The map covered all 11 bean chromosomes with an average distance of 3.6 cM between markers. A total of 13 QTL for agronomic and disease traits were consistently identified in different years. A major QTL WM3.1AN associated with white mold avoidance was validated on chromosome Pv03. The QTL is associated with disease avoidance traits such as canopy porosity, plant height, stay green stem trait, and maturity. Quantitative trait loci for maturity and canopy height also mapped to the same genomic region on Pv03. Finding strong associations between maturity, lodging, canopy height, and disease incidence offers alternative strategies to improve levels of white mold avoidance over greenhouse screening. The validation of the WM3.1AN, AP630 QTL for white mold avoidance should provide bean breeders with the opportunity to introgress avoidance traits into their germplasm.

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Genome‐wide association analysis of drought resistance based on seed germination vigor and germination rate at the bud stage in common bean

Chang

Wang

et al. 2021

Agronomy Journal

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Common bean (Phaseolus vulgaris L.) is an important food legume. However, drought influences its entire growth and development process and can cause yield losses. The influence of drought stress is the most severe in the bud stage. The major objective of our study was to identify a series of loci involved in drought stress response in the bud stage using association analysis. In this study, 361 common bean germplasms were used to investigate germination vigour (GV) and germination rate (GR) under distilled water and drought stress conditions.The common beans showed large variations in GV and GR, with GV ranging from 6.67% to 100% and 0 to 73.33% and GR ranging from 66.67% to 100% and 0 to 100% in distilled water and under drought stress, respectively. A genome-wide association study (GWAS) of 361 accessions was conducted using 3724159 single nucleotide polymorphisms (SNPs) and revealed 2 and 11 candidate SNPs associated with relative germination rate (RGR) and relative germination vigour (RGV), respectively. Three loci were collocated with loci previously reported as being related to drought tolerance. A total of 180 candidate genes were identified, many of which were related to ion transport and oxidation-reduction reactions. A major haplotype for RGV was identified on chromosome 6. These results provide new insight into the This article is protected by copyright. All rights reserved.3 genetic basis of drought tolerance in common bean at the bud stage and provide candidate SNPs and genes that can be used to accelerate the drought tolerance improvement of common bean.

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Genome‐Wide Association Study of Agronomic Traits in Common Bean

Cited by 90 publications

References 66 publications

Identification of QTL Associated with Drought Tolerance in Andean Common Bean

Identification of QTL Associated with Drought Tolerance in Andean Common Bean

Quantitative Trait Loci Analysis of White Mold Avoidance in Pinto Bean

Genome‐wide association analysis of drought resistance based on seed germination vigor and germination rate at the bud stage in common bean

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