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Zaleski-Cox M, Miklas PN, Soler-Garzón A, Hoyos-Villegas V. Automating high-throughput screening for anthracnose resistance in common bean using allele specific PCR. Plant Methods 2023; 19:102. [PMID: 37784144 PMCID: PMC10546687 DOI: 10.1186/s13007-023-01071-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 08/15/2023] [Indexed: 10/04/2023]
Abstract
BACKGROUND Common beans (Phaseolus vulgaris L.) provide important protein and calories globally. Anthracnose (Colletotrichum lindemuthianum (Sacc. & Magnus) Briosi & Cavara, 1889) is a major disease in common bean and causes significant yield losses in bean production areas. Screening for markers linked to known disease resistance genes provides useful information for plant breeders to develop improved common bean varieties. The Kompetitive Allele Specific PCR (KASP) assay is an affordable genetic screening technique that can be used to accelerate breeding programs, but manual DNA extraction and KASP assay preparation are time-consuming. Several KASP markers have been developed for genes involved in resistance to bean anthracnose, which can reduce yield by up to 100%, but their usefulness is hindered by the labor required to screen a significant number of bean lines. Our research objective was to develop publicly available protocols for DNA extraction and KASP assaying using a liquid handling robot (LHR) which would facilitate high-throughput genetic screening with less active human time required. Anthracnose resistance markers were used to compare manual and automated results. RESULTS The 12 bean anthracnose differential cultivars were screened for four anthracnose KASP markers linked to the resistance genes Co-1, Co-3 and Co-42 both by hand and with the use of an LHR. A protocol was written for DNA extraction and KASP assay thermocycling to implement the LHR. The LHR protocol reduced the active human screening time of 24 samples from 3h44 to 1h23. KASP calls were consistent across replicates but not always accurate for their known linked resistance genes, suggesting more specific markers still need to be developed. Using an LHR, information from KASP assays can be accumulated with little active human time. CONCLUSION Results suggest that LHRs can be used to expedite time-consuming and tedious lab work such as DNA extraction or PCR plate filling. Notably, LHRs can be used to prepare KASP assays for large sample sizes, facilitating higher throughput use of genetic marker screening tools.
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Affiliation(s)
| | - Phillip N Miklas
- Grain Legume Genetics and Physiology Research Unit, USDA-ARS, Prosser, WA, USA
| | - Alvaro Soler-Garzón
- Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA, USA
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Arriagada O, Arévalo B, Cabeza RA, Carrasco B, Schwember AR. Meta-QTL Analysis for Yield Components in Common Bean ( Phaseolus vulgaris L.). Plants (Basel) 2022; 12:117. [PMID: 36616246 PMCID: PMC9824219 DOI: 10.3390/plants12010117] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/15/2022] [Accepted: 12/17/2022] [Indexed: 06/17/2023]
Abstract
Common bean is one of the most important legumes produced and consumed worldwide because it is a highly valuable food for the human diet. However, its production is mainly carried out by small farmers, who obtain average grain yields below the potential yield of the species. In this sense, numerous mapping studies have been conducted to identify quantitative trait loci (QTL) associated with yield components in common bean. Meta-QTL (MQTL) analysis is a useful approach to combine data sets and for creating consensus positions for the QTL detected in independent studies. Consequently, the objective of this study was to perform a MQTL analysis to identify the most reliable and stable genomic regions associated with yield-related traits of common bean. A total of 667 QTL associated with yield-related traits reported in 21 different studies were collected. A total of 42 MQTL associated with yield-related traits were identified, in which the average confidence interval (CI) of the MQTL was 3.41 times lower than the CIs of the original QTL. Most of the MQTL (28) identified in this study contain QTL associated with yield and phenological traits; therefore, these MQTL can be useful in common bean breeding programs. Finally, a total of 18 candidate genes were identified and associated with grain yield within these MQTL, with functions related to ubiquitin ligase complex, response to auxin, and translation elongation factor activity.
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Affiliation(s)
- Osvin Arriagada
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
| | - Bárbara Arévalo
- Centro de Estudios en Alimentos Procesados, Talca 3460000, Chile
| | - Ricardo A. Cabeza
- Departamento de Producción Agrícola, Facultad de Ciencias Agrarias, Universidad de Talca, Talca 3460000, Chile
| | - Basilio Carrasco
- Centro de Estudios en Alimentos Procesados, Talca 3460000, Chile
| | - Andrés R. Schwember
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
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Özkan G, Haliloğlu K, Türkoğlu A, Özturk HI, Elkoca E, Poczai P. Determining Genetic Diversity and Population Structure of Common Bean ( Phaseolus vulgaris L.) Landraces from Türkiye Using SSR Markers. Genes (Basel) 2022; 13:1410. [PMID: 36011321 PMCID: PMC9407889 DOI: 10.3390/genes13081410] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 08/03/2022] [Accepted: 08/04/2022] [Indexed: 11/17/2022] Open
Abstract
Assessment of genetic diversity among different varieties helps to improve desired characteristics of crops, including disease resistance, early maturity, high yield, and resistance to drought. Molecular markers are one of the most effective tools for discovering genetic diversity that can increase reproductive efficiency. Simple sequence repeats (SSRs), which are codominant markers, are preferred for the determination of genetic diversity because they are highly polymorphic, multi-allelic, highly reproducible, and have good genome coverage. This study aimed to determine the genetic diversity of 40 common bean (Phaseolus vulgaris L.) landraces collected from the Ispir district located in the Northeast Anatolia region of Türkiye and five commercial varieties using SSR markers. The Twenty-seven SSR markers produced a total of 142 polymorphic bands, ranging from 2 (GATS91 and PVTT001) to 12 (BM153) alleles per marker, with an average number of 5.26 alleles. The gene diversity per marker varied between 0.37 and 0.87 for BM053 and BM153 markers, respectively. When heterozygous individuals are calculated proportional to the population, the heterozygosity ranged from 0.00 to 1.00, with an average of 0.30. The expected heterozygosity of the SSR locus ranged from 0.37 (BM053) to 0.88 (BM153), with an average of 0.69. Nei's gene diversity scored an average of 0.69. The polymorphic information content (PIC) values of SSR markers varied from 0.33 (BM053) to 0.86 (BM153), with an average of 0.63 per locus. The greatest genetic distance (0.83) was between lines 49, 50, 53, and cultivar Karacaşehir-90, while the shortest (0.08) was between lines 6 and 26. In cluster analysis using Nei's genetic distance, 45 common bean genotypes were divided into three groups and very little relationship was found between the genotypes and the geographical distances. In genetic structure analysis, three subgroups were formed, including local landraces and commercial varieties. The result confirmed that the rich diversity existing in Ispir bean landraces could be used as a genetic resource in designing breeding programs and may also contribute to Türkiye bean breeding programs.
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Affiliation(s)
- Güller Özkan
- Department of Biology, Faculty of Science, Ankara University, Ankara 06100, Türkiye
| | - Kamil Haliloğlu
- Department of Field Crops, Faculty of Agriculture, Ataturk University, Erzurum 25240, Türkiye
- Department of Biology, Faculty of Science, Cankiri Karatekin University, Çankırı 18200, Türkiye
| | - Aras Türkoğlu
- Department of Field Crops, Faculty of Agriculture, Necmettin Erbakan University, Konya 42310, Türkiye
| | - Halil Ibrahim Özturk
- Health Services Vocational School, Binali Yıldırım University, Erzincan 24100, Türkiye
| | - Erdal Elkoca
- Vocational High School, Department of Plant and Animal Production, İbrahim Çeçen University, Ağrı 04100, Türkiye
| | - Peter Poczai
- Botany Unit, Finnish Museum of Natural History, University of Helsinki, FI-00014 Helsinki, Finland
- Institute of Advanced Studies Kőszeg (iASK), H-9731 Kőszeg, Hungary
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Jia B, Conner RL, Penner WC, Zheng C, Cloutier S, Hou A, Xia X, You FM. Quantitative Trait Locus Mapping of Marsh Spot Disease Resistance in Cranberry Common Bean (Phaseolus vulgaris L.). Int J Mol Sci 2022; 23:ijms23147639. [PMID: 35886986 PMCID: PMC9324509 DOI: 10.3390/ijms23147639] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 07/01/2022] [Accepted: 07/07/2022] [Indexed: 02/01/2023] Open
Abstract
Common bean (Phaseolus vulgaris L.) is a food crop that is an important source of dietary proteins and carbohydrates. Marsh spot is a physiological disorder that diminishes seed quality in beans. Prior research suggested that this disease is likely caused by manganese (Mn) deficiency during seed development and that marsh spot resistance is controlled by at least four genes. In this study, genetic mapping was performed to identify quantitative trait loci (QTL) and the potential candidate genes associated with marsh spot resistance. All 138 recombinant inbred lines (RILs) from a bi-parental population were evaluated for marsh spot resistance during five years from 2015 to 2019 in sandy and heavy clay soils in Morden, Manitoba, Canada. The RILs were sequenced using a genotyping by sequencing approach. A total of 52,676 single nucleotide polymorphisms (SNPs) were identified and filtered to generate a high-quality set of 2066 SNPs for QTL mapping. A genetic map based on 1273 SNP markers distributed on 11 chromosomes and covering 1599 cm was constructed. A total of 12 stable and 4 environment-specific QTL were identified using additive effect models, and an additional two epistatic QTL interacting with two of the 16 QTL were identified using an epistasis model. Genome-wide scans of the candidate genes identified 13 metal transport-related candidate genes co-locating within six QTL regions. In particular, two QTL (QTL.3.1 and QTL.3.2) with the highest R2 values (21.8% and 24.5%, respectively) harbored several metal transport genes Phvul.003G086300, Phvul.003G092500, Phvul.003G104900, Phvul.003G099700, and Phvul.003G108900 in a large genomic region of 16.8–27.5 Mb on chromosome 3. These results advance the current understanding of the genetic mechanisms of marsh spot resistance in cranberry common bean and provide new genomic resources for use in genomics-assisted breeding and for candidate gene isolation and functional characterization.
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Affiliation(s)
- Bosen Jia
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (B.J.); (C.Z.); (S.C.)
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON K1N 6N5, Canada;
| | - Robert L. Conner
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada; (R.L.C.); (W.C.P.)
| | - Waldo C. Penner
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada; (R.L.C.); (W.C.P.)
| | - Chunfang Zheng
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (B.J.); (C.Z.); (S.C.)
| | - Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (B.J.); (C.Z.); (S.C.)
| | - Anfu Hou
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada; (R.L.C.); (W.C.P.)
- Correspondence: (A.H.); (F.M.Y.); Tel.: +1-204-822-7528 (A.H.); +1-613-759-1539 (F.M.Y.)
| | - Xuhua Xia
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON K1N 6N5, Canada;
| | - Frank M. You
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (B.J.); (C.Z.); (S.C.)
- Correspondence: (A.H.); (F.M.Y.); Tel.: +1-204-822-7528 (A.H.); +1-613-759-1539 (F.M.Y.)
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Haliloğlu K, Türkoğlu A, Öztürk HI, Özkan G, Elkoca E, Poczai P. iPBS-Retrotransposon Markers in the Analysis of Genetic Diversity among Common Bean (Phaseolus vulgaris L.) Germplasm from Türkiye. Genes (Basel) 2022; 13:genes13071147. [PMID: 35885928 PMCID: PMC9320141 DOI: 10.3390/genes13071147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 06/22/2022] [Accepted: 06/23/2022] [Indexed: 02/04/2023] Open
Abstract
Beans are legumes that play extremely important roles in human nutrition, serving as good sources of protein, vitamins, minerals, and antioxidants. In this study, we tried to elucidate the genetic diversity and population structure of 40 Turkish bean (Phaseolus vulgaris L.) local varieties and 5 commercial cultivars collected from 8 different locations in Erzurum-Ispir by using inter-primary binding site (iPBS) retrotransposon markers. For molecular characterization, the 26 most polymorphic iPBS primers were used; 52 bands per primer and 1350 bands in total were recorded. The mean polymorphism information content was 0.331. Various diversity indices, such as the mean effective allele number (0.706), mean Shannon’s information index (0.546), and gene diversity (0.361) revealed the presence of sufficient genetic diversity in the germplasm examined. Molecular analysis of variance (AMOVA) revealed that 67% of variation in bean germplasm was due to differences within populations. In addition, population structure analysis exposed all local and commercial bean varieties from five sub-populations. Expected heterozygosity values ranged between 0.1567 (the fourth sub-population) and 0.3210 (first sub-population), with an average value of 0.2103. In contrary, population differentiation measurement (Fst) was identified as 0.0062 for the first sub-population, 0.6372 for the fourth subpopulations. This is the first study to investigate the genetic diversity and population structure of bean germplasm in Erzurum-Ispir region using the iPBS-retrotransposon marker system. Overall, the current results showed that iPBS markers could be used consistently to elucidate the genetic diversity of local and commercial bean varieties and potentially be included in future studies examining diversity in a larger collection of local and commercial bean varieties from different regions.
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Affiliation(s)
- Kamil Haliloğlu
- Department of Field Crops, Faculty of Agriculture, Ataturk University, Erzurum 25240, Türkiye;
- Department of Biology, Faculty of Science, Cankiri Karatekin University, Çankırı 18200, Türkiye
| | - Aras Türkoğlu
- Department of Field Crops, Faculty of Agriculture, Necmettin Erbakan University, Konya 42310, Türkiye
- Correspondence: (A.T.); (P.P.)
| | - Halil Ibrahim Öztürk
- Health Services Vocational School, Binali Yıldırım University, Erzincan 24100, Türkiye;
| | - Güller Özkan
- Department of Biology, Faculty of Science, Ankara University, Ankara 06100, Türkiye;
| | - Erdal Elkoca
- Department of Herbal and Animal Production, Ibrahim Çeçen University, Ağrı 04100, Türkiye;
| | - Peter Poczai
- Botany Unit, Finnish Museum of Natural History, University of Helsinki, P.O. Box 7, FI-00014 Helsinki, Finland
- Institute of Advanced Studies Kőszeg (iASK), 9731 Kőszeg, Hungary
- Correspondence: (A.T.); (P.P.)
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Shao J, Hao Y, Wang L, Xie Y, Zhang H, Bai J, Wu J, Fu J. Development of a Model for Genomic Prediction of Multiple Traits in Common Bean Germplasm, Based on Population Structure. Plants (Basel) 2022; 11:1298. [PMID: 35631723 PMCID: PMC9144439 DOI: 10.3390/plants11101298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/08/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
Due to insufficient identification and in-depth investigation of existing common bean germplasm resources, it is difficult for breeders to utilize these valuable genetic resources. This situation limits the breeding and industrial development of the common bean (Phaseolus vulgaris L.) in China. Genomic prediction (GP) is a breeding method that uses whole-genome molecular markers to calculate the genomic estimated breeding value (GEBV) of candidate materials and select breeding materials. This study aimed to use genomic prediction to evaluate 15 traits in a collection of 628 common bean lines (including 484 landraces and 144 breeding lines) to determine a common bean GP model. The GP model constructed by landraces showed a moderate to high predictive ability (ranging from 0.59-0.88). Using all landraces as a training set, the predictive ability of the GP model for most traits was higher than that using the landraces from each of two subgene pools, respectively. Randomly selecting breeding lines as additional training sets together with landrace training sets to predict the remaining breeding lines resulted in a higher predictive ability based on principal components analysis. This study constructed a widely applicable GP model of the common bean based on the population structure, and encouraged the development of GP models to quickly aggregate excellent traits and accelerate utilization of germplasm resources.
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Affiliation(s)
- Jing Shao
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China;
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.H.); (L.W.); (Y.X.); (H.Z.)
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou 730070, China
| | - Yangfan Hao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.H.); (L.W.); (Y.X.); (H.Z.)
| | - Lanfen Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.H.); (L.W.); (Y.X.); (H.Z.)
| | - Yuxin Xie
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.H.); (L.W.); (Y.X.); (H.Z.)
| | - Hongwei Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.H.); (L.W.); (Y.X.); (H.Z.)
| | - Jiangping Bai
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China;
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou 730070, China
| | - Jing Wu
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China;
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.H.); (L.W.); (Y.X.); (H.Z.)
| | - Junjie Fu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.H.); (L.W.); (Y.X.); (H.Z.)
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Liu Y, Fang X, Tang T, Wang Y, Wu Y, Luo J, Wu H, Wang Y, Zhang J, Ruan R, Zhou M, Zhang K, Yi Z. Inflorescence Transcriptome Sequencing and Development of New EST-SSR Markers in Common Buckwheat ( Fagopyrum esculentum). Plants (Basel) 2022; 11:742. [PMID: 35336623 PMCID: PMC8950064 DOI: 10.3390/plants11060742] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 03/05/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
Common buckwheat (Fagopyrum esculentum M.) is known for its adaptability, good nutrition, and medicinal and health care value. However, genetic studies of buckwheat have been hindered by limited genomic resources and genetic markers. In this study, Illumina HiSeq 4000 high-throughput sequencing technology was used to sequence the transcriptome of green-flower common buckwheat (Gr) with coarse pedicels and white-flower Ukrainian daliqiao (UD) with fine pedicels. A total of 118,448 unigenes were obtained, with an average length of 1248 bp and an N50 of 1850 bp. A total of 39,432 differentially expressed genes (DEGs) were identified, and the DEGs of the porphyrins and chlorophyll metabolic pathway had significantly upregulated expression in Gr. Then, a total of 17,579 sequences containing SSR loci were detected, and 20,756 EST-SSR loci were found. The distribution frequency of EST-SSR in the transcriptome was 17.52%, and the average distribution density was 8.21 kb. A total of 224 pairs of primers were randomly selected for synthesis; 35 varieties of common buckwheat and 13 varieties of Tartary buckwheat were verified through these primers. The clustering results well verified the previous conclusion that common buckwheat and Tartary buckwheat had a distant genetic relationship. The EST-SSR markers identified and developed in this study will be helpful to enrich the transcriptome information and marker-assisted selection breeding of buckwheat.
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Affiliation(s)
- Yang Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (Y.L.); (X.F.); (T.T.); (Y.W.); (Y.W.); (J.L.); (H.W.); (Y.W.); (J.Z.); (R.R.)
| | - Xiaomei Fang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (Y.L.); (X.F.); (T.T.); (Y.W.); (Y.W.); (J.L.); (H.W.); (Y.W.); (J.Z.); (R.R.)
| | - Tian Tang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (Y.L.); (X.F.); (T.T.); (Y.W.); (Y.W.); (J.L.); (H.W.); (Y.W.); (J.Z.); (R.R.)
| | - Yudong Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (Y.L.); (X.F.); (T.T.); (Y.W.); (Y.W.); (J.L.); (H.W.); (Y.W.); (J.Z.); (R.R.)
| | - Yinhuan Wu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (Y.L.); (X.F.); (T.T.); (Y.W.); (Y.W.); (J.L.); (H.W.); (Y.W.); (J.Z.); (R.R.)
| | - Jinyu Luo
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (Y.L.); (X.F.); (T.T.); (Y.W.); (Y.W.); (J.L.); (H.W.); (Y.W.); (J.Z.); (R.R.)
| | - Haotian Wu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (Y.L.); (X.F.); (T.T.); (Y.W.); (Y.W.); (J.L.); (H.W.); (Y.W.); (J.Z.); (R.R.)
| | - Yingqian Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (Y.L.); (X.F.); (T.T.); (Y.W.); (Y.W.); (J.L.); (H.W.); (Y.W.); (J.Z.); (R.R.)
| | - Jian Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (Y.L.); (X.F.); (T.T.); (Y.W.); (Y.W.); (J.L.); (H.W.); (Y.W.); (J.Z.); (R.R.)
| | - Renwu Ruan
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (Y.L.); (X.F.); (T.T.); (Y.W.); (Y.W.); (J.L.); (H.W.); (Y.W.); (J.Z.); (R.R.)
| | - Meiliang Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
| | - Kaixuan Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
| | - Zelin Yi
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (Y.L.); (X.F.); (T.T.); (Y.W.); (Y.W.); (J.L.); (H.W.); (Y.W.); (J.Z.); (R.R.)
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Delfini J, Moda-Cirino V, Dos Santos Neto J, Zeffa DM, Nogueira AF, Ribeiro LAB, Ruas PM, Gepts P, Gonçalves LSA. Genome-wide association study for grain mineral content in a Brazilian common bean diversity panel. Theor Appl Genet 2021; 134:2795-2811. [PMID: 34027567 DOI: 10.1007/s00122-021-03859-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/10/2021] [Indexed: 06/12/2023]
Abstract
QTNs significantly associated to nine mineral content in grains of common bean were identified. The accumulation of favorable alleles was associated with a gradually increasing nutrient content in the grain. Biofortification is one of the strategies developed to address malnutrition in developing countries, the aim of which is to improve the nutritional content of crops. The common bean (Phaseolus vulgaris L.), a staple food in several African and Latin American countries, has excellent nutritional attributes and is considered a strong candidate for biofortification. The objective of this study was to identify genomic regions associated with nutritional content in common bean grains using 178 Mesoamerican accessions belonging to a Brazilian Diversity Panel (BDP) and 25,011 good-quality single nucleotide polymorphisms. The BDP was phenotyped in three environments for nine nutrients (phosphorus, potassium, calcium, magnesium, copper, manganese, sulfur, zinc, and iron) using four genome-wide association multi-locus methods. To obtain more accurate results, only quantitative trait nucleotides (QTNs) that showed repeatability (i.e., those detected at least twice using different methods or environments) were considered. Forty-eight QTNs detected for the nine minerals showed repeatability and were considered reliable. Pleiotropic QTNs and overlapping genomic regions surrounding the QTNs were identified, demonstrating the possible association between the deposition mechanisms of different nutrients in grains. The accumulation of favorable alleles in the same accession was associated with a gradually increasing nutrient content in the grain. The BDP proved to be a valuable source for association studies. The investigation of different methods and environments showed the reliability of markers associated with minerals. The loci identified in this study will potentially contribute to the improvement of Mesoamerican common beans, particularly carioca and black beans, the main groups consumed in Brazil.
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Affiliation(s)
- Jessica Delfini
- Plant Breeding, Instituto de Desenvolvimento Rural do Paraná-IDR-Paraná-Emater (IDR-Paraná), Londrina, Brazil
- Agronomy Department, Universidade Estadual de Londrina (UEL), Londrina, Brazil
| | - Vânia Moda-Cirino
- Plant Breeding, Instituto de Desenvolvimento Rural do Paraná-IDR-Paraná-Emater (IDR-Paraná), Londrina, Brazil
| | - José Dos Santos Neto
- Plant Breeding, Instituto de Desenvolvimento Rural do Paraná-IDR-Paraná-Emater (IDR-Paraná), Londrina, Brazil
- Agronomy Department, Universidade Estadual de Londrina (UEL), Londrina, Brazil
| | - Douglas Mariani Zeffa
- Plant Breeding, Instituto de Desenvolvimento Rural do Paraná-IDR-Paraná-Emater (IDR-Paraná), Londrina, Brazil
- Agronomy Department, Universidade Estadual de Maringá, Maringá, Paraná, Brazil
| | - Alison Fernando Nogueira
- Plant Breeding, Instituto de Desenvolvimento Rural do Paraná-IDR-Paraná-Emater (IDR-Paraná), Londrina, Brazil
- Agronomy Department, Universidade Estadual de Londrina (UEL), Londrina, Brazil
| | - Luriam Aparecida Brandão Ribeiro
- Plant Breeding, Instituto de Desenvolvimento Rural do Paraná-IDR-Paraná-Emater (IDR-Paraná), Londrina, Brazil
- Agronomy Department, Universidade Estadual de Londrina (UEL), Londrina, Brazil
| | - Paulo Maurício Ruas
- Biology Department, Universidade Estadual de Londrina (UEL), Londrina, Brazil
| | - Paul Gepts
- Department of Plant Sciences, Section of Crop and Ecosystem Sciences, University of California, Davis, CA, USA
| | - Leandro Simões Azeredo Gonçalves
- Agronomy Department, Universidade Estadual de Londrina (UEL), Londrina, Brazil.
- Agronomy Department, Universidade Estadual de Maringá, Maringá, Paraná, Brazil.
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Martin CJ, Torkamaneh D, Arif M, Pauls KP. Genome-Wide Association Study of Seed Folate Content in Common Bean. Front Plant Sci 2021; 12:696423. [PMID: 34531882 PMCID: PMC8438126 DOI: 10.3389/fpls.2021.696423] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 08/03/2021] [Indexed: 06/10/2023]
Abstract
Plant-derived folates (Vitamin B9) are essential components of the human diet. They provide one-carbon units that are required for the synthesis of nucleic acids and proteins, and folate deficiency is associated with numerous adverse health conditions. The development of high-folate cultivars of common bean (Phaseolus vulgaris L.) and other staple crops is an important tool to combat folate deficiency. A population of 96 P. vulgaris accessions, representing major North American market classes, was grown in 2 years in Ontario, Canada. The population was genotyped for 5,361 molecular markers with an Illumina Infinium platform. Total folate was extracted from mature seeds using the tri-enzyme extraction method and quantified based on a microbiological assay with Lactobacillus rhamnosus. Significant genetic diversity for folate content was observed among the population in both years of study, and folate content had a range 113-222 μg per 100 g of seeds. Quantitative trait loci (QTL) for seed folate content were identified based on a genome-wide association study (GWAS). Six QTL were identified on Chr. 4, 6, 8, and 11, with three in each year of field trials. Both QTL on Chr. 11 occurred in genomic regions that were syntenic to seed folate QTL detected in previous work with P. vulgaris, Z. mays, and O. sativa. Candidate genes were identified for these QTL that might be targets for the development of molecular markers for selecting P. vulgaris cultivars with improved seed folate content. This work reports the largest survey of genetic diversity for seed folate content in P. vulgaris and identified several genotypes, including SCN4, Bat 93, OAC Redstar, and Pompadour 1014, that would be useful for breeding beans with higher than average folate levels.
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Affiliation(s)
- C. Joe Martin
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - Davoud Torkamaneh
- Département de Phytologie, Université Laval, Québec City, QC, Canada
| | - Muhammad Arif
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - Karl Peter Pauls
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
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10
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de Carvalho Paulino JF, de Almeida CP, Song Q, Carbonell SAM, Chiorato AF, Benchimol-Reis LL. Genetic diversity and inter-gene pool introgression of Mesoamerican Diversity Panel in common beans. J Appl Genet 2021; 62:585-600. [PMID: 34386968 DOI: 10.1007/s13353-021-00657-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 07/15/2021] [Accepted: 08/02/2021] [Indexed: 10/20/2022]
Abstract
Brazil is among the largest producers and consumers of common bean (Phaseolus vulgaris L.) and can be considered a secondary center of diversity for the species. The aim of this study was to estimate the genetic diversity, population structure, and relationships among 288 common bean accessions in an American Diversity Panel (ADP) genotyped with 4,042 high-quality single nucleotide polymorphisms (SNPs). The results showed inter-gene pool hybridization (hybrids) between the two main gene pools (i.e., Mesoamerican and Andean), based on principal component analysis (PCA), discriminant analysis of principal components (DAPC), and STRUCTURE analysis. The genetic diversity parameters showed that the Mesoamerican group has higher values of diversity and allelic richness in comparison with the Andean group. Considering the optimal clusters (K), clustering was performed according to the type of grain (i.e., market group), the institution of origin, the period of release, and agronomic traits. A new subset was selected and named the Mesoamerican Diversity Panel (MDP), with 205 Mesoamerican accessions. Analysis of molecular variance (AMOVA) showed low genetic variance between the two panels (i.e., ADP and MDP) with the highest percentage of the limited variance among accessions in each group. The ADP showed occurrence of high genetic differentiation between populations (i.e., Mesoamerican and Andean) and introgression between gene pools in hybrids based on a set of diagnostic SNPs. The MDP showed better linkage disequilibrium (LD) decay. The availability of genetic variation from inter-gene pool hybridizations presents a potential opportunity for breeders towards the development of superior common bean cultivars.
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Affiliation(s)
| | - Caléo Panhoca de Almeida
- Common Bean Genetic Group, Natural Center of Plant Genetics, Agronomic Institute (IAC), Campinas, SP, Brazil
| | - Qijian Song
- Soybean Genomics and Improvement Lab, USDA-ARS, Beltsville, MD, USA
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11
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Tormena CD, Campos RCS, Marcheafave GG, Edward Bruns R, Scarminio IS, Pauli ED. Authentication of carioca common bean cultivars (Phaseolus vulgaris L.) using digital image processing and chemometric tools. Food Chem 2021; 364:130349. [PMID: 34175626 DOI: 10.1016/j.foodchem.2021.130349] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/31/2021] [Accepted: 06/09/2021] [Indexed: 01/10/2023]
Abstract
Bean authentication can result in higher quality products for commerce. Partial least squares discriminant analysis (PLS-DA) was applied to digital images in order to develop a methodology that allows the non-destructive discrimination of three Phaseolus vulgaris L. cultivars (Agro ANfc9, IPR-Andorinha, and IPR-Sabiá) having different technological characteristics. Principal component analysis resulted in a separation of these cultivars, but with a certain amount of overlap. Supervised analysis showed that three PLS1-DA models, each for two cultivars, was moderately better than the simultaneous treatment of all three cultivars (PLS2-DA). Permutation test evaluated statistical significance of PLS-DA models. The classification models were more accurate for Agro ANfc9 and IPR-Sabiá cultivars than for IPR-Andorinha. The Agro ANfc9-IPR-Sabiá model correctly classified 100% of the two bean classes in both training and test sets. This analytical strategy is fast, inexpensive, environmentally friendly, and can be applied for bean quality control helping cultivar authenticity for commerce.
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12
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Chacón-Sánchez MI, Martínez-Castillo J, Duitama J, Debouck DG. Gene Flow in Phaseolus Beans and Its Role as a Plausible Driver of Ecological Fitness and Expansion of Cultigens. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.618709] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The genus Phaseolus, native to the Americas, is composed of more than eighty wild species, five of which were domesticated in pre-Columbian times. Since the beginning of domestication events in this genus, ample opportunities for gene flow with wild relatives have existed. The present work reviews the extent of gene flow in the genus Phaseolus in primary and secondary areas of domestication with the aim of illustrating how this evolutionary force may have conditioned ecological fitness and the widespread adoption of cultigens. We focus on the biological bases of gene flow in the genus Phaseolus from a spatial and time perspective, the dynamics of wild-weedy-crop complexes in the common bean and the Lima bean, the two most important domesticated species of the genus, and the usefulness of genomic tools to detect inter and intraspecific introgression events. In this review we discuss the reproductive strategies of several Phaseolus species, the factors that may favor outcrossing rates and evidence suggesting that interspecific gene flow may increase ecological fitness of wild populations. We also show that wild-weedy-crop complexes generate genetic diversity over which farmers are able to select and expand their cultigens outside primary areas of domestication. Ultimately, we argue that more studies are needed on the reproductive biology of the genus Phaseolus since for most species breeding systems are largely unknown. We also argue that there is an urgent need to preserve wild-weedy-crop complexes and characterize the genetic diversity generated by them, in particular the genome-wide effects of introgressions and their value for breeding programs. Recent technological advances in genomics, coupled with agronomic characterizations, may make a large contribution.
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Parry C, Wang YW, Lin SW, Barchenger DW. Reproductive compatibility in Capsicum is not necessarily reflected in genetic or phenotypic similarity between species complexes. PLoS One 2021; 16:e0243689. [PMID: 33760824 PMCID: PMC8508556 DOI: 10.1371/journal.pone.0243689] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 02/17/2021] [Indexed: 11/18/2022] Open
Abstract
Wild relatives of domesticated Capsicum represent substantial
genetic diversity and thus sources of traits of potential interest. Furthermore,
the hybridization compatibility between members of Capsicum
species complexes remains unresolved. Improving our understanding of the
relationship between Capsicum species relatedness and their
ability to form hybrids is a highly pertinent issue. Through the development of
novel interspecific hybrids in this study, we demonstrate interspecies
compatibility is not necessarily reflected in relatedness according to
established Capsicum genepool complexes. Based on a phylogeny
constructed by genotyping using simple sequence repeat (SSR) markers and with a
portion of the waxy locus, and through principal component
analysis (PCA) of phenotypic data, we clarify the relationships among wild and
domesticated Capsicum species. Together, the phylogeny and
hybridization studies provide evidence for the misidentification of a number of
species from the World Vegetable Center genebank included in this study. The
World Vegetable Center holds the largest collection of Capsicum
genetic material globally, therefore this may reflect a wider issue in the
misidentification of Capsicum wild relatives. The findings
presented here provide insight into an apparent disconnect between compatibility
and relatedness in the Capsicum genus, which will be valuable
in identifying candidates for future breeding programs.
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Affiliation(s)
- Catherine Parry
- Department of Biology and Biochemistry, University of Bath, Claverton
Down, Bath, United Kingdom
| | - Yen-Wei Wang
- World Vegetable Center, Shanhua, Tainan, 74151, Taiwan
| | - Shih-wen Lin
- World Vegetable Center, Shanhua, Tainan, 74151, Taiwan
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Delfini J, Moda-Cirino V, dos Santos Neto J, Ruas PM, Sant’Ana GC, Gepts P, Gonçalves LSA. Population structure, genetic diversity and genomic selection signatures among a Brazilian common bean germplasm. Sci Rep 2021; 11:2964. [PMID: 33536468 PMCID: PMC7859210 DOI: 10.1038/s41598-021-82437-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 01/07/2021] [Indexed: 01/30/2023] Open
Abstract
Brazil is the world's largest producer of common bean. Knowledge of the genetic diversity and relatedness of accessions adapted to Brazilian conditions is of great importance for the conservation of germplasm and for directing breeding programs aimed at the development of new cultivars. In this context, the objective of this study was to analyze the genetic diversity, population structure, and linkage disequilibrium (LD) of a diversity panel consisting of 219 common bean accessions, most of which belonging to the Mesoamerican gene pool. Genotyping by sequencing (GBS) of these accessions allowed the identification of 49,817 SNPs with minor allele frequency > 0.05. Of these, 17,149 and 12,876 were exclusive to the Mesoamerican and Andean pools, respectively, and 11,805 SNPs could differentiate the two gene pools. Further the separation according to the gene pool, bayesian analysis of the population structure showed a subdivision of the Mesoamerican accessions based on the origin and color of the seed tegument. LD analysis revealed the occurrence of long linkage blocks and low LD decay with physical distance between SNPs (LD half decay in 249 kb, corrected for population structure and relatedness). The GBS technique could effectively characterize the Brazilian common bean germplasms, and the diversity panel used in this study may be of great use in future genome-wide association studies.
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Affiliation(s)
- Jessica Delfini
- grid.411400.00000 0001 2193 3537Agronomy Department, Universidade Estadual de Londrina (UEL), Londrina, 86051-900 Brazil ,Plant Breeding, Instituto de Desenvolvimento Rural do Paraná-Iapar-Emater (IDR-Paraná), Londrina, 86047-902 Brazil
| | - Vânia Moda-Cirino
- Plant Breeding, Instituto de Desenvolvimento Rural do Paraná-Iapar-Emater (IDR-Paraná), Londrina, 86047-902 Brazil
| | - José dos Santos Neto
- grid.411400.00000 0001 2193 3537Agronomy Department, Universidade Estadual de Londrina (UEL), Londrina, 86051-900 Brazil ,Plant Breeding, Instituto de Desenvolvimento Rural do Paraná-Iapar-Emater (IDR-Paraná), Londrina, 86047-902 Brazil
| | - Paulo Maurício Ruas
- grid.411400.00000 0001 2193 3537Biology Department, Universidade Estadual de Londrina (UEL), Londrina, 86051-900 Brazil
| | | | - Paul Gepts
- grid.27860.3b0000 0004 1936 9684Section of Crop and Ecosystem Sciences, Department of Plant Sciences, University of California, Davis, 95616-8780 USA
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15
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de Almeida CP, Paulino JFDC, Morais Carbonell SA, Chiorato AF, Song Q, Di Vittori V, Rodriguez M, Papa R, Benchimol-Reis LL. Genetic Diversity, Population Structure, and Andean Introgression in Brazilian Common Bean Cultivars after Half a Century of Genetic Breeding. Genes (Basel) 2020; 11:E1298. [PMID: 33143347 PMCID: PMC7694079 DOI: 10.3390/genes11111298] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 10/27/2020] [Accepted: 10/28/2020] [Indexed: 12/29/2022] Open
Abstract
Brazil is the largest consumer and third highest producer of common beans (Phaseolus vulgaris L.) worldwide. Since the 1980s, the commercial Carioca variety has been the most consumed in Brazil, followed by Black and Special beans. The present study evaluates genetic diversity and population structure of 185 Brazilian common bean cultivars using 2827 high-quality single-nucleotide polymorphisms (SNPs). The Andean allelic introgression in the Mesoamerican accessions was investigated, and a Carioca panel was tested using an association mapping approach. The results distinguish the Mesoamerican from the Andean accessions, with a prevalence of Mesoamerican accessions (94.6%). When considering the commercial classes, low levels of genetic differentiation were seen, and the Carioca group showed the lowest genetic diversity. However, gain in gene diversity and allelic richness was seen for the modern Carioca cultivars. A set of 1060 'diagnostic SNPs' that show alternative alleles between the pure Mesoamerican and Andean accessions were identified, which allowed the identification of Andean allelic introgression events and shows that there are putative introgression segments in regions enriched with resistance genes. Finally, genome-wide association studies revealed SNPs significantly associated with flowering time, pod maturation, and growth habit, showing that the Carioca Association Panel represents a powerful tool for crop improvements.
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Affiliation(s)
- Caléo Panhoca de Almeida
- Centro de Pesquisa em Recursos Genéticos Vegetais, Instituto Agronômico (IAC), Campinas, São Paulo 13075-630, Brazil; (J.F.d.C.P.); (L.L.B.-R.)
| | - Jean Fausto de Carvalho Paulino
- Centro de Pesquisa em Recursos Genéticos Vegetais, Instituto Agronômico (IAC), Campinas, São Paulo 13075-630, Brazil; (J.F.d.C.P.); (L.L.B.-R.)
| | | | - Alisson Fernando Chiorato
- Centro de Grãos e Fibras, Instituto Agronômico (IAC), Campinas, São Paulo 13075-630, Brazil; (S.A.M.C.); (A.F.C.)
| | - Qijian Song
- Soybean Genomics and Improvement Laboratory, US Department of Agriculture–Agricultural Research Service (USDA-ARS), Beltsville, MD 20705, USA;
| | - Valerio Di Vittori
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica dele Marche, 60131 Ancona, Italy; (V.D.V.); (R.P.)
- Max-Planck-Institute of Molecular Plant Physiology, Am Müehlenberg 1, 14476 Potsdam-Golm, Germany
| | - Monica Rodriguez
- Dipartimento di Agraria, Università degli Studi di Sassari, 07100 Sassari, Italy;
- Centro per la Cobservazione e Valorizzazione della Biodiversità Vegetale (CBV), Università degli Studi di Sassari, 07040 Alghero, Italy
| | - Roberto Papa
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica dele Marche, 60131 Ancona, Italy; (V.D.V.); (R.P.)
| | - Luciana Lasry Benchimol-Reis
- Centro de Pesquisa em Recursos Genéticos Vegetais, Instituto Agronômico (IAC), Campinas, São Paulo 13075-630, Brazil; (J.F.d.C.P.); (L.L.B.-R.)
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16
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Ye H, Wu J, Wang Z, Hou H, Gao Y, Han W, Ru W, Sun G, Wang Y. Population genetic variation characterization of the boreal tree Acer ginnala in Northern China. Sci Rep 2020; 10:13515. [PMID: 32782277 PMCID: PMC7419535 DOI: 10.1038/s41598-020-70444-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 07/24/2020] [Indexed: 11/09/2022] Open
Abstract
Genetic diversity and differentiation are revealed particularly through spatio-temporal environmental heterogeneity. Acer ginnala, as a deciduous shrub/small tree, is a foundation species in many terrestrial ecosystems of Northern China. Owing to its increased use as an economic resource, this species has been in the vulnerability. Therefore, the elucidations of the genetic differentiation and influence of environmental factors on A. ginnala are very critical for its management and future utilization strategies. In this study, high genetic diversity and differentiation occurred in A. ginnala, which might be resulted from its pollination mechanism and species characteristics. Compared with the species level, relatively low genetic diversity was detected at the population level that might be the cause for its vulnerability. There was no significant relationship between genetic and geographical distances, while a significant correlation existed between genetic and environmental distances. Among nineteen climate variables, Annual Mean Temperature (bio1), Mean Diurnal Range (bio2), Isothermality (bio3), Temperature Seasonality (bio4), Precipitation of Wettest Month (bio13), Precipitation Seasonality (bio15), and Precipitation of Warmest Quarter (bio18) could explain the substantial levels of genetic variation (> 40%) in this species. The A. ginnala populations were isolated into multi-subpopulations by the heterogeneous climate conditions, which subsequently promoted the genetic divergence. Climatic heterogeneity played an important role in the pattern of genetic differentiation and population distribution of A. ginnala across a relatively wide range in Northern China. These would provide some clues for the conservation and management of this vulnerable species.
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Affiliation(s)
- Hang Ye
- College of Life Science, Shanxi Normal University, Linfen, 041000, Shanxi, China
| | - Jiahui Wu
- College of Life Science, Shanxi Normal University, Linfen, 041000, Shanxi, China.,Changzhi University, Changzhi, 046011, Shanxi, China
| | - Zhi Wang
- College of Life Science, Shanxi Normal University, Linfen, 041000, Shanxi, China
| | - Huimin Hou
- College of Life Science, Shanxi Normal University, Linfen, 041000, Shanxi, China
| | - Yue Gao
- College of Life Science, Shanxi Normal University, Linfen, 041000, Shanxi, China
| | - Wei Han
- College of Life Science, Shanxi Normal University, Linfen, 041000, Shanxi, China
| | - Wenming Ru
- Changzhi University, Changzhi, 046011, Shanxi, China.
| | - Genlou Sun
- Department of Biology, Saint Mary's University, Halifax, NS, B3H3C3, Canada.
| | - Yiling Wang
- College of Life Science, Shanxi Normal University, Linfen, 041000, Shanxi, China.
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17
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Fiore MC, Raimondo FM, Mercati F, Digangi I, Sunseri F, Scialabba A. Preserving Biodiversity in Marginal Rural Areas: Assessment of Morphological and Genetic Variability of a Sicilian Common Bean Germplasm Collection. Plants (Basel) 2020; 9:E989. [PMID: 32759817 PMCID: PMC7463873 DOI: 10.3390/plants9080989] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 07/31/2020] [Accepted: 08/01/2020] [Indexed: 11/17/2022]
Abstract
The historical cultivation of common bean (Phaseolus vulgaris L.) has resulted in the development of local populations/cultivars in restricted Italian rural areas. Many common bean landraces, still cultivated in small mountain areas from Sicily, have become outdated and endangered due to the commercial varieties spreading. These accessions are poorly known but often represent a genetic heritage to be preserved and enhanced. The ex situ conservation of fifty-seven Sicilian common bean landraces was carried out at the "Living Plants Germplasm Bank" at Ucria (Messina, Italy), founded by the Nebrodi Regional Park, together with the "Sicilian Plant Germplasm Repository" of University of Palermo (SPGR/PA). To assess the germplasm genetic diversity, nineteen morphological traits and eight Simple Sequence Repeats (SSRs) were used. Genetic distances among landraces were calculated to construct a clustering tree by using unweighted pair group method arithmetic (UPGMA). Seed germplasm diversity of Sicilian common bean varied from 80.7% to 93.3%, based on six seed descriptors and six leaf, flower, and pod descriptors, respectively, while cluster genetic analysis depicted a clear separation among all the 57 landraces. Principal coordinates (PCoA) and STRUCTURE analyses showed a prevalent rate of admixture between Mesoamerican and Andean gene pools in Sicilian common bean collection, confirming its heterogeneity. The observed high level of diversity evidenced the needs to adopt accurate criterion to plan a definitive ex situ germplasm collection to share agrobiodiversity with local farmers and to avoid any further loss of genetic resources in rural and protected areas.
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Affiliation(s)
- Maria Carola Fiore
- Council for Agricultural Research and Economics Research Centre for Plant Protection and Certification (S.S. 113 km 245,500), 90011 Bagheria, Italy
| | | | - Francesco Mercati
- Institute of Biosciences and Bioresources (IBBR), National Research Council, Corso Calatafimi 414, 90129 Palermo, Italy;
| | - Ignazio Digangi
- Living Plants Germplasm Bank of Nebrodi, Contrada Pirato, 98060 Ucria (ME), Italy;
| | - Francesco Sunseri
- Department of Agraria, University Mediterranea of Reggio Calabria, Località Feo di Vito snc, 89124 Reggio Calabria, Italy;
| | - Anna Scialabba
- Department of Biological, Chemical and Pharmaceutical Science and Technologies (STEBICEF), University of Palermo, Via Archirafi 38, 90123 Palermo, Italy;
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Wilker J, Navabi A, Rajcan I, Marsolais F, Hill B, Torkamaneh D, Pauls KP. Agronomic Performance and Nitrogen Fixation of Heirloom and Conventional Dry Bean Varieties Under Low-Nitrogen Field Conditions. Front Plant Sci 2019; 10:952. [PMID: 31404343 PMCID: PMC6676800 DOI: 10.3389/fpls.2019.00952] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 07/09/2019] [Indexed: 05/26/2023]
Abstract
Common beans (Phaseolus vulgaris) form a relationship with nitrogen-fixing rhizobia and through a process termed symbiotic nitrogen fixation (SNF) which provides them with a source of nitrogen. However, beans are considered poor nitrogen fixers, and modern production practices involve routine use of N fertilizer, which leads to the down-regulation of SNF. High-yielding, conventionally bred bean varieties are developed using conventional production practices and selection criteria, typically not including SNF efficiency, and may have lost this trait over decades of modern breeding. In contrast, heirloom bean genotypes were developed before the advent of modern production practices and may represent an underutilized pool of genetics which could be used to improve SNF. This study compared the SNF capacity under low-N field conditions, of collections of heirloom varieties with and conventionally bred dry bean varieties. The heirloom-conventional panel (HCP) consisted of 42 genotypes from various online seed retailers or from the University of Guelph Bean Breeding program seedbank. The HCP was genotyped using a single nucleotide polymorphism (SNP) array to investigate genetic relatedness within the panel. Field trials were conducted at three locations in ON, Canada from 2014 to 2015 and various agronomic and seed composition traits were measured, including capacity for nitrogen fixation (using the natural abundance method to measure seed N isotope ratios). Significant variation for SNF was found in the panel. However, on average, heirloom genotypes did not fix significantly more nitrogen than conventionally bred varieties. However, five heirloom genotypes fixed >60% of their nitrogen from the atmosphere. Yield (kg ha-1) was not significantly different between heirloom and conventional genotypes, suggesting that incorporating heirloom genotypes into a modern breeding program would not negatively impact yield. Nitrogen fixation was significantly higher among Middle American genotypes than among Andean genotypes, confirming previous findings. The best nitrogen fixing line was Coco Sophie, a European heirloom white bean whose genetic makeup is admixed between the Andean and Middle American genepools. Heirloom genotypes represent a useful source of genetics to improve SNF in modern bean breeding.
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Affiliation(s)
- Jennifer Wilker
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - Alireza Navabi
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - Istvan Rajcan
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - Frédéric Marsolais
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON, Canada
| | - Brett Hill
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB, Canada
| | - Davoud Torkamaneh
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - K. Peter Pauls
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
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