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Fofana B, Soto-Cerda B, Zaidi M, Main D, Fillmore S. Genome-wide genetic architecture for plant maturity and drought tolerance in diploid potatoes. Front Genet 2024; 14:1306519. [PMID: 38357658 PMCID: PMC10864671 DOI: 10.3389/fgene.2023.1306519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 12/18/2023] [Indexed: 02/16/2024] Open
Abstract
Cultivated potato (Solanum tuberosum) is known to be highly susceptible to drought. With climate change and its frequent episodes of drought, potato growers will face increased challenges to achieving their yield goals. Currently, a high proportion of untapped potato germplasm remains within the diploid potato relatives, and the genetic architecture of the drought tolerance and maturity traits of diploid potatoes is still unknown. As such, a panel of 384 ethyl methanesulfonate-mutagenized diploid potato clones were evaluated for drought tolerance and plant maturity under field conditions. Genome-wide association studies (GWAS) were conducted to dissect the genetic architecture of the traits. The results obtained from the genetic structure analysis of the panel showed five main groups and seven subgroups. Using the Genome Association and Prediction Integrated Tool-mixed linear model GWAS statistical model, 34 and 17 significant quantitative trait nucleotides (QTNs) were found associated with maturity and drought traits, respectively. Chromosome 5 carried most of the QTNs, some of which were also detected by using the restricted two-stage multi-locus multi-allele-GWAS haploblock-based model, and two QTNs were found to be pleiotropic for both maturity and drought traits. Using the non-parametric U-test, one and three QTNs, with 5.13%-7.4% phenotypic variations explained, showed favorable allelic effects that increase the maturity and drought trait values. The quantitaive trait loci (QTLs)/QTNs associated with maturity and drought trait were found co-located in narrow (0.5-1 kb) genomic regions with 56 candidate genes playing roles in plant development and senescence and in abiotic stress responses. A total of 127 potato clones were found to be late maturing and tolerant to drought, while nine were early to moderate-late maturing and tolerant to drought. Taken together, the data show that the studied germplasm panel and the identified candidate genes are prime genetic resources for breeders and biologists in conventional breeding and targeted gene editing as climate adaptation tools.
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Affiliation(s)
- Bourlaye Fofana
- Charlottetown Research and Development Centre, Agriculture and Agri-Food Canada, Charlottetown, PE, Canada
| | - Braulio Soto-Cerda
- Departamento de Ciencias Agropecuarias y Acuícolas, Universidad Católica de Temuco, Temuco, Chile
- Núcleo de Investigación en Producción Alimentaria, Facultad de Recursos Naturales, Universidad Católica de Temuco, Temuco, Chile
| | - Moshin Zaidi
- Charlottetown Research and Development Centre, Agriculture and Agri-Food Canada, Charlottetown, PE, Canada
| | - David Main
- Charlottetown Research and Development Centre, Agriculture and Agri-Food Canada, Charlottetown, PE, Canada
| | - Sherry Fillmore
- Kentville Research and Development Centre, Agriculture and Agri-Food Canada, Kentville, NS, Canada
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dos Santos CC, de Andrade LRB, do Carmo CD, de Oliveira EJ. Development of cassava core collections based on morphological and agronomic traits and SNPS markers. FRONTIERS IN PLANT SCIENCE 2023; 14:1250205. [PMID: 37745996 PMCID: PMC10511765 DOI: 10.3389/fpls.2023.1250205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 08/21/2023] [Indexed: 09/26/2023]
Abstract
Cassava (Manihot esculenta Crantz) holds significant importance as one of the world's key starchy crop species. This study aimed to develop core collections by utilizing both phenotypic data (15 quantitative and 33 qualitative descriptors) and genotypic data (20,023 single-nucleotide polymorphisms) obtained from 1,486 cassava accessions. Six core collections were derived through two optimization strategies based on genetic distances: Average accession-to-nearest-entry and Average entry-to-nearest-entry, along with combinations of phenotypic and genotypic data. The quality of the core collections was evaluated by assessing genetic parameters such as genetic diversity Shannon-Weaver Index, inbreeding (Fis), observed (Ho), and expected (Hs) heterozygosity. While the selection of accessions varied among the six core collections, a seventh collection (consolidated collection) was developed, comprising accessions selected by at least two core collections. Most collections exhibited genetic parameters similar to the complete collection, except for those developed by the Average accession-to-nearest-entry algorithm. However, the variations in the maximum and minimum values of Ho, Hs, and Fis parameters closely resembled the complete collection. The consolidated collection and the collection constructed using genotypic data and the Average entry-to-nearest-entry algorithm (GenEN) retained the highest number of alleles (>97%). Although the differences were not statistically significant (above 5%), the consolidated collection demonstrated a distribution profile and mean trait values most similar to the complete collection, with a few exceptions. The Shannon-Weaver Index of qualitative traits exhibited variations exceeding ±10% when compared to the complete collection. Principal component analysis revealed that the consolidated collection selected cassava accessions with a more uniform dispersion in all four quadrants compared to the other core collections. These findings highlight the development of optimized and valuable core collections for efficient breeding programs and genomic association studies.
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Affiliation(s)
- Caroline Cardoso dos Santos
- Centro de Ciências Agrárias, Ambientais e Biológicas, Universidade Federal do Recôncavo da Bahia, Cruz das Almas, Bahia, Brazil
| | | | - Cátia Dias do Carmo
- Centro de Ciências Agrárias, Ambientais e Biológicas, Universidade Federal do Recôncavo da Bahia, Cruz das Almas, Bahia, Brazil
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Cerón-Souza I, Delgadillo-Duran D, Polo-Murcia SM, Sarmiento-Naizaque ZX, Reyes-Herrera PH. Prioritizing Colombian plant genetic resources for investment in research using indicators about the geographic origin, vulnerability status, economic benefits, and food security importance. BIODIVERSITY AND CONSERVATION 2023; 32:2221-2261. [PMID: 37255861 PMCID: PMC10195663 DOI: 10.1007/s10531-023-02599-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 03/07/2023] [Accepted: 03/23/2023] [Indexed: 06/01/2023]
Abstract
Germplasm banks are the most significant repository for plant genetic resources for food and agriculture (PGRFA) worldwide. Despite their strategic importance, national germplasm banks of tropical megadiverse developing countries such as Colombia have extremely limited funds. Therefore, making strategic decisions about research investment is essential. Here, we designed a data-driven approach to build an index that sorts Colombian PGRFA into three groups: high, medium, or low priority, based on four pillars of information from open-access databases and aligned with the sustainable goals of no poverty and zero hunger: Geographic origin, vulnerability status, economic benefits, and food security importance. We analyzed 345 PGRFA using the index, separating them into two groups, 275 already conserved in the Colombian germplasm bank (BGVCOL group) and 70 not currently conserved in the BGVCOL (NCB group). We used fuzzy logic to classify each PGRFA by each pillar and integrate it to obtain a priority index. Missing data for native crops were frequent in the BGVCOL group. Therefore we adopted an imputation strategy to fill the gaps and calculated the uncertainty. After applying the index, PGRFA with higher priority were 24 (8.72%) from the BGVCOL (i.e., 15 potatoes, three tomatoes, two tree tomatoes, pineapple, cocoa, papaya, and yacon) and one from NCB (i.e., coffee). We concluded that this methodology successfully prioritized PGRFA in Colombia and shows the big holes of knowledge for future research and alternatives to improve this index. The versatility of this methodology could be helpful in other genebanks with budget limitations for research investment. Supplementary Information The online version contains supplementary material available at 10.1007/s10531-023-02599-7.
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Affiliation(s)
- I. Cerón-Souza
- CI Tibaitatá, Corporación Colombiana de Investigación Agropecuaria, AGROSAVIA, Km 14 via Mosquera, Bogotá, Colombia
| | - D. Delgadillo-Duran
- CI Tibaitatá, Corporación Colombiana de Investigación Agropecuaria, AGROSAVIA, Km 14 via Mosquera, Bogotá, Colombia
| | - S. M. Polo-Murcia
- CI Tibaitatá, Corporación Colombiana de Investigación Agropecuaria, AGROSAVIA, Km 14 via Mosquera, Bogotá, Colombia
| | - Z. X. Sarmiento-Naizaque
- CI Tibaitatá, Corporación Colombiana de Investigación Agropecuaria, AGROSAVIA, Km 14 via Mosquera, Bogotá, Colombia
| | - P. H. Reyes-Herrera
- CI Tibaitatá, Corporación Colombiana de Investigación Agropecuaria, AGROSAVIA, Km 14 via Mosquera, Bogotá, Colombia
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Berdugo-Cely JA, Céron-Lasso MDS, Yockteng R. Phenotypic and molecular analyses in diploid and tetraploid genotypes of Solanum tuberosum L. reveal promising genotypes and candidate genes associated with phenolic compounds, ascorbic acid contents, and antioxidant activity. FRONTIERS IN PLANT SCIENCE 2023; 13:1007104. [PMID: 36743552 PMCID: PMC9889998 DOI: 10.3389/fpls.2022.1007104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 12/08/2022] [Indexed: 06/18/2023]
Abstract
Potato tubers contain biochemical compounds with antioxidant properties that benefit human health. However, the genomic basis of the production of antioxidant compounds in potatoes has largely remained unexplored. Therefore, we report the first genome-wide association study (GWAS) based on 4488 single nucleotide polymorphism (SNP) markers and the phenotypic evaluation of Total Phenols Content (TPC), Ascorbic Acid Content (AAC), and Antioxidant Activity (AA) traits in 404 diverse potato genotypes (84 diploids and 320 tetraploids) conserved at the Colombian germplasm bank that administers AGROSAVIA. The concentration of antioxidant compounds correlated to the skin tuber color and ploidy level. Especially, purple-blackish tetraploid tubers had the highest TPC (2062.41 ± 547.37 mg GAE), while diploid pink-red tubers presented the highest AA (DDPH: 14967.1 ± 4687.79 μmol TE; FRAP: 2208.63 ± 797.35 mg AAE) and AAC (4.52 mg ± 0.68 AA). The index selection allowed us to choose 20 promising genotypes with the highest values for the antioxidant compounds. Genome Association mapping identified 58 SNP-Trait Associations (STAs) with single-locus models and 28 Quantitative Trait Nucleotide (QTNs) with multi-locus models associated with the evaluated traits. Among models, eight STAs/QTNs related to TPC, AAC, and AA were detected in common, flanking seven candidate genes, from which four were pleiotropic. The combination in one population of diploid and tetraploid genotypes enabled the identification of more genetic associations. However, the GWAS analysis implemented independently in populations detected some regions in common between diploids and tetraploids not detected in the mixed population. Candidate genes have molecular functions involved in phenolic compounds, ascorbic acid biosynthesis, and antioxidant responses concerning plant abiotic stress. All candidate genes identified in this study can be used for further expression analysis validation and future implementation in marker-assisted selection pre-breeding platforms targeting fortified materials. Our study further revealed the importance of potato germplasm conserved in national genebanks, such as AGROSAVIA's, as a valuable genetic resource to improve existing potato varieties.
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Affiliation(s)
- Jhon A. Berdugo-Cely
- Corporación Colombiana de Investigación Agropecuaria-AGROSAVIA, Centro de Investigación Turipaná, Km 13 vía Montería-Cereté, Montería, Córdoba, Colombia
- Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA), Centro de Investigación Tibaitatá, Km 13 vía Mosquera-Bogotá, Mosquera, Cundinamarca, Colombia
| | - María del Socorro Céron-Lasso
- Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA), Centro de Investigación Tibaitatá, Km 13 vía Mosquera-Bogotá, Mosquera, Cundinamarca, Colombia
| | - Roxana Yockteng
- Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA), Centro de Investigación Tibaitatá, Km 13 vía Mosquera-Bogotá, Mosquera, Cundinamarca, Colombia
- Institut de Systématique, Evolution, Biodiversité-UMR-CNRS 7205, National Museum of Natural History, Paris, France
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Behn A, Lizana C, Zapata F, Gonzalez A, Reyes-Díaz M, Fuentes D. Phenolic and anthocyanin content characterization related to genetic diversity analysis of Solanum tuberosum subsp. tuberosum Chilotanum Group in southern Chile. FRONTIERS IN PLANT SCIENCE 2023; 13:1045894. [PMID: 36704150 PMCID: PMC9872146 DOI: 10.3389/fpls.2022.1045894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/16/2022] [Indexed: 06/18/2023]
Abstract
The potato (Solanum tuberosum L) is one of the four most important crops worldwide in production and consumption. It originated from South America along the Andes, where six hotspots of diversity known as subcenters of origin are described from Venezuela to Chiloe Island in Chile, and where the greatest diversity of potatoes in the world is found. Today, the use of ancestral genetic resources has gained significant relevance, recovering and producing foods with a greater nutrient content and beneficial to human health. Therefore, native potatoes possess a set of characteristics with great potential for use in potato breeding guided primarily to produce better feed, especially potatoes of the Chilotanum Group that are easily crossed with conventional varieties. The primary objective of this study was to evaluate 290 accessions of S. tuberosum subsp tuberosum belonging to the Chilotanum Group using a set of molecular markers and correlate them to its phenotypic traits for future use in breeding programs. For this purpose, 290 accessions were analysed through 22 specific microsatellites described previously, correlating them with flesh and skin colour, total phenolic content, and anthocyanin content. A division into groups considering all the 290 accessions resulted in two clusters using STRUCTURE analysis and seven different genetic clusters using UPGMA. The latter exhibited common phenotypic characteristics as well as anthocyanin content, strongly supporting a correlation between phenotypic traits and the genetic fingerprint. These results will enable breeders to focus on the development of potatoes with high polyphenol and anthocyanin content.
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Affiliation(s)
- Anita Behn
- Instituto de Producción y Sanidad Vegetal, Facultad de Ciencias Agrarias y Alimentarias, Universidad Austral de Chile, Valdivia, Chile
| | - Carolina Lizana
- Instituto de Producción y Sanidad Vegetal, Facultad de Ciencias Agrarias y Alimentarias, Universidad Austral de Chile, Valdivia, Chile
| | - Felipe Zapata
- Biocomputing and Applied Genetics, Center for Systems Biotechnology, Fraunhofer Chile Research Foundation, Santiago, Chile
| | - Alvaro Gonzalez
- Biocomputing and Applied Genetics, Center for Systems Biotechnology, Fraunhofer Chile Research Foundation, Santiago, Chile
| | - Marjorie Reyes-Díaz
- Departamento de Ciencias Químicas y Recursos Naturales, Facultad de Ingeniería y Ciencias, Universidad de La Frontera, Temuco, Chile
| | - Derie Fuentes
- Biocomputing and Applied Genetics, Center for Systems Biotechnology, Fraunhofer Chile Research Foundation, Santiago, Chile
- Centro de Biotecnología de Sistemas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
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Manrique-Carpintero NC, Berdugo-Cely JA, Cerón-Souza I, Lasso-Paredes Z, Reyes-Herrera PH, Yockteng R. Defining a diverse core collection of the Colombian Central Collection of potatoes: a tool to advance research and breeding. FRONTIERS IN PLANT SCIENCE 2023; 14:1046400. [PMID: 37180391 PMCID: PMC10173156 DOI: 10.3389/fpls.2023.1046400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 03/14/2023] [Indexed: 05/16/2023]
Abstract
The highly diverse Colombian Central Collection (CCC) of cultivated potatoes is the most important source of genetic variation for breeding and the agricultural development of this staple crop in Colombia. Potato is the primary source of income for more than 100.000 farming families in Colombia. However, biotic and abiotic challenges limit crop production. Furthermore, climate change, food security, and malnutrition constraints call for adaptive crop development to be urgently addressed. The clonal CCC of potatoes contains 1,255 accessions - an extensive collection size that limits its optimal assessment and use. Our study evaluated different collection sizes from the whole clonal collection to define the best core collection that captures the total genetic diversity of this unique collection, to support a characterization more cost-effectively. Initially, we genotyped 1,141 accessions from the clonal collection and 20 breeding lines using 3,586 genome-wide polymorphic markers to study CCC's genetic diversity. The analysis of molecular variance confirmed the CCC's diversity with a significant population structure (Phi=0.359; p-value=0.001). Three main genetic pools were identified within this collection (CCC_Group_A, CCC_Group_B1, and CCC_Group_B2), and the commercial varieties were located across the pools. The ploidy level was the main driver of pool identification, followed by a robust representation of accessions from Phureja and Andigenum cultivar groups based on former taxonomic classifications. We also found divergent heterozygosity values within genetic groups, with greater diversity in genetic groups with tetraploids (CCC_Group_B1: 0.37, and CCC_Group_B2: 0.53) than in diploid accessions (CCC_Group_A: 0.14). We subsequently generated one mini-core collection size of 3 percent (39 entries) and three further core collections sizes of 10, 15, and 20 percent (i.e., 129, 194, and 258 entries, respectively) from the total samples genotyped. As our results indicated that genetic diversity was similar across the sampled core collection sizes compared to the main collection, we selected the smallest core collection size of 10 percent. We expect this 10 percent core collection to be an optimal tool for discovering and evaluating functional diversity in the genebank to advance potato breeding and agricultural-related studies. This study also lays the foundations for continued CCC curation by evaluating duplicity and admixing between accessions, completing the digitalization of data, and ploidy determination using chloroplast count.
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Affiliation(s)
| | - Jhon A. Berdugo-Cely
- Corporación Colombiana de Investigación Agropecuaria-AGROSAVIA, Centro de Investigación Tibaitatá, Mosquera, Colombia
- Corporación Colombiana de Investigación Agropecuaria-AGROSAVIA, Centro de Investigación Turipaná, Montería, Colombia
| | - Ivania Cerón-Souza
- Corporación Colombiana de Investigación Agropecuaria-AGROSAVIA, Centro de Investigación Tibaitatá, Mosquera, Colombia
| | - Zahara Lasso-Paredes
- Corporación Colombiana de Investigación Agropecuaria-AGROSAVIA, Centro de Investigación Tibaitatá, Mosquera, Colombia
| | - Paula H. Reyes-Herrera
- Corporación Colombiana de Investigación Agropecuaria-AGROSAVIA, Centro de Investigación Tibaitatá, Mosquera, Colombia
| | - Roxana Yockteng
- Corporación Colombiana de Investigación Agropecuaria-AGROSAVIA, Centro de Investigación Tibaitatá, Mosquera, Colombia
- Institut de Systématique, Evolution, Biodiversité-UMR-CNRS 7205, National Museum of Natural History, Paris, France
- *Correspondence: Roxana Yockteng,
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Hu J, Mei M, Jin F, Xu J, Duan S, Bian C, Li G, Wang X, Jin L. Phenotypic variability and genetic diversity analysis of cultivated potatoes in China. FRONTIERS IN PLANT SCIENCE 2022; 13:954162. [PMID: 36212356 PMCID: PMC9541749 DOI: 10.3389/fpls.2022.954162] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
Phenotypic evaluation and molecular biotechnology are both important in the identification and utilization of crop germplasm resources. In this study, the phenotypic variation and genetic diversity of 149 main potato cultivars in China were investigated with 12 phenotypic traits and 24 SSR markers. The coefficient of variation of 12 phenotypic traits ranged from 12.11% to 156.93%. The results of SSR markers exhibited a relatively high level of genetic variation (Na =5.458 ± 1.499, Ne =3.300 ± 1.087, I =1.397 ± 0.298, Ho =0.797 ± 0.178, He = 0.660 ± 0.117, and PIC=0.702 ± 0.087). Population structure and phylogenetic tree analysis divided the varieties into three subgroups. The results indicated that ninety percent of the molecular variance was attributed to within-group differences, and the remaining 10% was attributed to variation among groups. Consistent with previous report, alleles of the STI032 marker were significantly associated with tuber starch content and growth period traits in the population. The results of this study could facilitate the utilization of potato germplasm resources, molecular genetic breeding and improvement.
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Affiliation(s)
- Jun Hu
- Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crops, Ministry of Agriculture and Rural Affairs of the People’s Republic of China, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Meng Mei
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Fang Jin
- National Agro-Tech Extension and Service Center, Ministry of Agriculture and Rural Affairs of the People’s Republic of China, Beijing, China
| | - Jianfei Xu
- Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crops, Ministry of Agriculture and Rural Affairs of the People’s Republic of China, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shaoguang Duan
- Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crops, Ministry of Agriculture and Rural Affairs of the People’s Republic of China, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chunsong Bian
- Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crops, Ministry of Agriculture and Rural Affairs of the People’s Republic of China, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guangcun Li
- Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crops, Ministry of Agriculture and Rural Affairs of the People’s Republic of China, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiyao Wang
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Liping Jin
- Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crops, Ministry of Agriculture and Rural Affairs of the People’s Republic of China, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
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Tiwari JK, Buckseth T, Zinta R, Bhatia N, Dalamu D, Naik S, Poonia AK, Kardile HB, Challam C, Singh RK, Luthra SK, Kumar V, Kumar M. Germplasm, Breeding, and Genomics in Potato Improvement of Biotic and Abiotic Stresses Tolerance. FRONTIERS IN PLANT SCIENCE 2022; 13:805671. [PMID: 35197996 PMCID: PMC8859313 DOI: 10.3389/fpls.2022.805671] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 01/17/2022] [Indexed: 05/23/2023]
Abstract
Potato is one of the most important food crops in the world. Late blight, viruses, soil and tuber-borne diseases, insect-pests mainly aphids, whiteflies, and potato tuber moths are the major biotic stresses affecting potato production. Potato is an irrigated and highly fertilizer-responsive crop, and therefore, heat, drought, and nutrient stresses are the key abiotic stresses. The genus Solanum is a reservoir of genetic diversity, however, a little fraction of total diversity has been utilized in potato breeding. The conventional breeding has contributed significantly to the development of potato varieties. In recent years, a tremendous progress has been achieved in the sequencing technologies from short-reads to long-reads sequence data, genomes of Solanum species (i.e., pan-genomics), bioinformatics and multi-omics platforms such as genomics, transcriptomics, proteomics, metabolomics, ionomics, and phenomics. As such, genome editing has been extensively explored as a next-generation breeding tool. With the available high-throughput genotyping facilities and tetraploid allele calling softwares, genomic selection would be a reality in potato in the near future. This mini-review covers an update on germplasm, breeding, and genomics in potato improvement for biotic and abiotic stress tolerance.
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Affiliation(s)
| | | | - Rasna Zinta
- ICAR-Central Potato Research Institute, Shimla, India
| | - Nisha Bhatia
- ICAR-Central Potato Research Institute, Shimla, India
- School of Biotechnology, Shoolini University, Solan, India
| | - Dalamu Dalamu
- ICAR-Central Potato Research Institute, Shimla, India
| | - Sharmistha Naik
- ICAR-Central Potato Research Institute, Shimla, India
- ICAR-National Research Centre for Grapes, Pune, India
| | - Anuj K. Poonia
- School of Biotechnology, Shoolini University, Solan, India
| | - Hemant B. Kardile
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, United States
| | - Clarissa Challam
- ICAR-Central Potato Research Institute, Regional Station, Shillong, India
| | | | - Satish K. Luthra
- ICAR-Central Potato Research Institute, Regional Station, Meerut, India
| | - Vinod Kumar
- ICAR-Central Potato Research Institute, Shimla, India
| | - Manoj Kumar
- ICAR-Central Potato Research Institute, Regional Station, Meerut, India
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Ivanov AA, Ukladov EO, Golubeva TS. Phytophthora infestans: An Overview of Methods and Attempts to Combat Late Blight. J Fungi (Basel) 2021; 7:1071. [PMID: 34947053 PMCID: PMC8707485 DOI: 10.3390/jof7121071] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 12/10/2021] [Accepted: 12/11/2021] [Indexed: 12/20/2022] Open
Abstract
Phytophthora infestans (Mont.) de Bary is one of the main pathogens in the agricultural sector. The most affected are the Solanaceae species, with the potato (Solanum tuberosum) and the tomato (Solanum lycopersicum) being of great agricultural importance. Ornamental Solanaceae can also host the pests Petunia spp., Calibrachoa spp., as well as the wild species Solanum dulcamara, Solanum sarrachoides, etc. Annual crop losses caused by this pathogen are highly significant. Although the interaction between P. infestans and the potato has been investigated for a long time, further studies are still needed. This review summarises the basic approaches in the fight against the late blight over the past 20 years and includes four sections devoted to methods of control: (1) fungicides; (2) R-gene-based resistance of potato species; (3) RNA interference approaches; (4) other approaches to control P. infestans. Based on the latest advances, we have provided a description of the significant advantages and disadvantages of each approach.
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Affiliation(s)
- Artemii A. Ivanov
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia;
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia;
| | - Egor O. Ukladov
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia;
| | - Tatiana S. Golubeva
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia;
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia;
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Singh B, Goutam U, Kukreja S, Sharma J, Sood S, Bhardwaj V. Potato biofortification: an effective way to fight global hidden hunger. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2297-2313. [PMID: 34744367 PMCID: PMC8526655 DOI: 10.1007/s12298-021-01081-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/16/2021] [Accepted: 09/22/2021] [Indexed: 06/03/2023]
Abstract
Hidden hunger is leading to extensive health problems in the developing world. Several strategies could be used to reduce the micronutrient deficiencies by increasing the dietary uptake of essential micronutrients. These include diet diversification, pharmaceutical supplementation, food fortification and crop biofortification. Among all, crop biofortification is the most sustainable and acceptable strategy to overcome the global issue of hidden hunger. Since most of the people suffering from micronutrient deficiencies, have monetary issues and are dependent on staple crops to fulfil their recommended daily requirements of various essential micronutrients. Therefore, increasing the micronutrient concentrations in cost effective staple crops seems to be an effective solution. Potato being the world's most consumed non-grain staple crop with enormous industrial demand appears to be an ideal candidate for biofortification. It can be grown in different climatic conditions, provide high yield, nutrition and dry matter in lesser time. In addition, huge potato germplasm have natural variations related to micronutrient concentrations, which can be utilized for its biofortification. This review discuss the current scenario of micronutrient malnutrition and various strategies that could be used to overcome it. The review also shed a light on the genetic variations present in potato germplasm and suggest effective ways to incorporate them into modern high yielding potato varieties.
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Affiliation(s)
- Baljeet Singh
- Division of Crop Improvement and Seed Technology, Central Potato Research Institute, Shimla, India
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, India
| | - Umesh Goutam
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, India
| | - Sarvjeet Kukreja
- Department of Agronomy, Lovely Professional University, Phagwara, India
| | - Jagdev Sharma
- Division of Crop Production, Central Potato Research Institute, Shimla, India
| | - Salej Sood
- Division of Crop Improvement and Seed Technology, Central Potato Research Institute, Shimla, India
| | - Vinay Bhardwaj
- Division of Crop Improvement and Seed Technology, Central Potato Research Institute, Shimla, India
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11
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Peña C, Palomeque L, Restrepo‐Sánchez L, Kushalappa A, Mosquera T, Narváez‐Cuenca C. Variation of mineral contents with nutritional interest in a collection of
Solanum tuberosum
group Phureja tubers. Int J Food Sci Technol 2021. [DOI: 10.1111/ijfs.15115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Clara Peña
- Departamento de Química Universidad Nacional de Colombia sede Bogotá, Edificio 451 Bogotá Colombia
| | - Liliam Palomeque
- Departamento de Química Universidad Nacional de Colombia sede Bogotá, Edificio 451 Bogotá Colombia
| | | | - Ajjamada Kushalappa
- Plant Science Department McGill University Sainte‐Anne‐de‐Bellevue QC H9X3V9 Canada
| | - Teresa Mosquera
- Departamento de Agronomía Facultad de Ciencias Agrarias Universidad Nacional de Colombia sede Bogotá, Edificio 500 Bogotá Colombia
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12
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Valkov VT, Gargano D, Cardi T, Scotti N. Plastid Transformation in Potato: An Important Source of Nutrition and Industrial Materials. Methods Mol Biol 2021; 2317:247-256. [PMID: 34028773 DOI: 10.1007/978-1-0716-1472-3_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
For a long time, plastid transformation has been a routine technology only in tobacco due to lack of effective selection and regeneration protocols, and, for some species, due to inefficient recombination using heterologous flanking regions in transformation vectors. Nevertheless, the availability of this technology to economically important crops offers new possibilities in plant breeding to manage pathogen resistance or improve nutritional value. Herein we describe an efficient plastid transformation protocol for potato (Solanum tuberosum subsp. tuberosum), achieved by the optimization of the tissue culture procedures and using transformation vectors carrying homologous potato flanking sequences. This protocol allowed to obtain up to one shoot per shot, an efficiency comparable to that usually accomplished in tobacco. Further, the method described in this chapter has been successfully used to regenerate potato transplastomic plants expressing recombinant GFP protein in chloroplasts and amyloplasts or long double-stranded RNAs for insect pest control.
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Affiliation(s)
- Vladimir T Valkov
- CNR-IBBR, National Research Council of Italy, Institute of Biosciences and BioResources, Research Division Portici, Portici (NA), Italy
| | - Daniela Gargano
- CNR-IBBR, National Research Council of Italy, Institute of Biosciences and BioResources, Research Division Portici, Portici (NA), Italy
| | - Teodoro Cardi
- CNR-IBBR, National Research Council of Italy, Institute of Biosciences and BioResources, Research Division Portici, Portici (NA), Italy.,CREA-OF, Research Centre for Vegetable and Ornamental Crops, Pontecagnano (SA), Italy
| | - Nunzia Scotti
- CNR-IBBR, National Research Council of Italy, Institute of Biosciences and BioResources, Research Division Portici, Portici (NA), Italy.
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13
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Genome-wide approaches for the identification of markers and genes associated with sugarcane yellow leaf virus resistance. Sci Rep 2021; 11:15730. [PMID: 34344928 PMCID: PMC8333424 DOI: 10.1038/s41598-021-95116-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 07/19/2021] [Indexed: 11/10/2022] Open
Abstract
Sugarcane yellow leaf (SCYL), caused by the sugarcane yellow leaf virus (SCYLV) is a major disease affecting sugarcane, a leading sugar and energy crop. Despite damages caused by SCYLV, the genetic base of resistance to this virus remains largely unknown. Several methodologies have arisen to identify molecular markers associated with SCYLV resistance, which are crucial for marker-assisted selection and understanding response mechanisms to this virus. We investigated the genetic base of SCYLV resistance using dominant and codominant markers and genotypes of interest for sugarcane breeding. A sugarcane panel inoculated with SCYLV was analyzed for SCYL symptoms, and viral titer was estimated by RT-qPCR. This panel was genotyped with 662 dominant markers and 70,888 SNPs and indels with allele proportion information. We used polyploid-adapted genome-wide association analyses and machine-learning algorithms coupled with feature selection methods to establish marker-trait associations. While each approach identified unique marker sets associated with phenotypes, convergences were observed between them and demonstrated their complementarity. Lastly, we annotated these markers, identifying genes encoding emblematic participants in virus resistance mechanisms and previously unreported candidates involved in viral responses. Our approach could accelerate sugarcane breeding targeting SCYLV resistance and facilitate studies on biological processes leading to this trait.
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14
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Garreta L, Cerón‐Souza I, Palacio MR, Reyes‐Herrera PH. MultiGWAS: An integrative tool for Genome Wide Association Studies in tetraploid organisms. Ecol Evol 2021; 11:7411-7426. [PMID: 34188823 PMCID: PMC8216910 DOI: 10.1002/ece3.7572] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 12/27/2022] Open
Abstract
The genome-wide association studies (GWASs) are essential to determine the genetic bases of either ecological or economic phenotypic variation across individuals within populations of the model and nonmodel organisms. For this research question, the GWAS replication testing different parameters and models to validate the results' reproducibility is common. However, straightforward methodologies that manage both replication and tetraploid data are still missing. To solve this problem, we designed the MultiGWAS, a tool that does GWAS for diploid and tetraploid organisms by executing in parallel four software packages, two designed for polyploid data (GWASpoly and SHEsis) and two designed for diploid data (GAPIT and TASSEL). MultiGWAS has several advantages. It runs either in the command line or in a graphical interface; it manages different genotype formats, including VCF. Moreover, it allows control for population structure, relatedness, and several quality control checks on genotype data. Besides, MultiGWAS can test for additive and dominant gene action models, and, through a proprietary scoring function, select the best model to report its associations. Finally, it generates several reports that facilitate identifying false associations from both the significant and the best-ranked association Single Nucleotide Polymorphisms (SNPs) among the four software packages. We tested MultiGWAS with public tetraploid potato data for tuber shape and several simulated data under both additive and dominant models. These tests demonstrated that MultiGWAS is better at detecting reliable associations than using each of the four software packages individually. Moreover, the parallel analysis of polyploid and diploid software that only offers MultiGWAS demonstrates its utility in understanding the best genetic model behind the SNP association in tetraploid organisms. Therefore, MultiGWAS probed to be an excellent alternative for wrapping GWAS replication in diploid and tetraploid organisms in a single analysis environment.
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Affiliation(s)
- Luis Garreta
- Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA)CI TibaitatáBogotaColombia
| | - Ivania Cerón‐Souza
- Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA)CI TibaitatáBogotaColombia
| | | | - Paula H. Reyes‐Herrera
- Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA)CI TibaitatáBogotaColombia
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15
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Parra-Galindo MA, Soto-Sedano JC, Mosquera-Vásquez T, Roda F. Pathway-based analysis of anthocyanin diversity in diploid potato. PLoS One 2021; 16:e0250861. [PMID: 33914830 PMCID: PMC8084248 DOI: 10.1371/journal.pone.0250861] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 04/14/2021] [Indexed: 12/21/2022] Open
Abstract
Anthocyanin biosynthesis is one of the most studied pathways in plants due to the important ecological role played by these compounds and the potential health benefits of anthocyanin consumption. Given the interest in identifying new genetic factors underlying anthocyanin content we studied a diverse collection of diploid potatoes by combining a genome-wide association study and pathway-based analyses. By using an expanded SNP dataset, we identified candidate genes that had not been associated with anthocyanin variation in potatoes, namely a Myb transcription factor, a Leucoanthocyanidin dioxygenase gene and a vacuolar membrane protein. Importantly, a genomic region in chromosome 10 harbored the SNPs with strongest associations with anthocyanin content in GWAS. Some of these SNPs were associated with multiple anthocyanin compounds and therefore could underline the existence of pleiotropic genes or anthocyanin biosynthetic clusters. We identified multiple anthocyanin homologs in this genomic region, including four transcription factors and five enzymes that could be governing anthocyanin variation. For instance, a SNP linked to the phenylalanine ammonia-lyase gene, encoding the first enzyme in the phenylpropanoid biosynthetic pathway, was associated with all of the five anthocyanins measured. Finally, we combined a pathway analysis and GWAS of other agronomic traits to identify pathways related to anthocyanin biosynthesis in potatoes. We found that methionine metabolism and the production of sugars and hydroxycinnamic acids are genetically correlated to anthocyanin biosynthesis. The results contribute to the understanding of anthocyanins regulation in potatoes and can be used in future breeding programs focused on nutraceutical food.
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Affiliation(s)
| | - Johana Carolina Soto-Sedano
- Departamento de Biología, Facultad de Ciencias, Universidad Nacional de Colombia, Sede Bogotá, Bogotá, Colombia
| | - Teresa Mosquera-Vásquez
- Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Sede Bogotá, Bogotá, Colombia
| | - Federico Roda
- Max Planck Tandem Group, Facultad de Ciencias, Universidad Nacional de Colombia, Sede Bogotá, Bogotá, Colombia
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16
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Pandey J, Scheuring DC, Koym JW, Coombs J, Novy RG, Thompson AL, Holm DG, Douches DS, Miller JC, Vales MI. Genetic diversity and population structure of advanced clones selected over forty years by a potato breeding program in the USA. Sci Rep 2021; 11:8344. [PMID: 33863959 PMCID: PMC8052460 DOI: 10.1038/s41598-021-87284-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 03/24/2021] [Indexed: 01/12/2023] Open
Abstract
Knowledge regarding genetic diversity and population structure of breeding materials is essential for crop improvement. The Texas A&M University Potato Breeding Program has a collection of advanced clones selected and maintained in-vitro over a 40-year period. Little is known about its genetic makeup and usefulness for the current breeding program. In this study, 214 potato clones were genotyped with the Infinium Illumina 22 K V3 Potato Array. After filtering, a total of 10,106 single nucleotide polymorphic (SNP) markers were used for analysis. Heterozygosity varied by SNP, with an overall average of 0.59. Three groups of tetraploid clones primarily based on potato market classes, were detected using STRUCTURE software and confirmed by discriminant analysis of principal components.
The highest coefficient of differentiation observed between the groups was 0.14. Signatures of selection were uncovered in genes controlling potato flesh and skin color, length of plant cycle and tuberization, and carbohydrate metabolism. A core set of 43 clones was obtained using Core Hunter 3 to develop a sub-collection that retains similar genetic diversity as the whole population, minimize redundancies, and facilitates long-term conservation of genetic resources. The comprehensive molecular characterization of our breeding clone bank collection contributes to understanding the genetic diversity of existing potato resources. This analysis could be applied to other breeding programs and assist in the selection of parents, fingerprinting, protection, and management of the breeding collections.
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Affiliation(s)
- Jeewan Pandey
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843-2133, USA
| | - Douglas C Scheuring
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843-2133, USA
| | - Jeffrey W Koym
- Texas A&M AgriLife Research and Extension Center, Lubbock, TX, 79403, USA
| | - Joseph Coombs
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - Richard G Novy
- USDA-Agricultural Research Service, Small Grains and Potato Germplasm Research, Aberdeen, ID, 83210, USA
| | - Asunta L Thompson
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - David G Holm
- San Luis Valley Research Center, Department of Horticulture and Landscape Architecture, Colorado State University, Center, CO, 81125, USA
| | - David S Douches
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - J Creighton Miller
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843-2133, USA
| | - M Isabel Vales
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843-2133, USA.
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17
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Lee KJ, Sebastin R, Cho GT, Yoon M, Lee GA, Hyun DY. Genetic Diversity and Population Structure of Potato Germplasm in RDA-Genebank: Utilization for Breeding and Conservation. PLANTS (BASEL, SWITZERLAND) 2021; 10:752. [PMID: 33921437 PMCID: PMC8068792 DOI: 10.3390/plants10040752] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/08/2021] [Accepted: 04/08/2021] [Indexed: 11/17/2022]
Abstract
Potato (Solanum tuberosum L.) is an important staple food and economic crop in many countries. It is of critical importance to understand the genetic diversity and population structure for effective collection, conservation, and utilization of potato germplasm. Thus, the objective of the present study was to investigate the genetic diversity and population structure of potato germplasm conserved in the National Agrobiodiversity Center (NAC) of South Korea to provide basic data for future preservation and breeding of potato genetic resources. A total of 24 simple sequence repeat (SSR) markers were used to assess the genetic diversity and population structure of 482 potato accessions. A total of 257 alleles were detected, with an average of 10.71 alleles per locus. Analysis of molecular variance showed that 97% of allelic diversity was attributed to individual accessions within the population, while only 3% was distributed among populations. Results of genetic structure analysis based on STRUCTURE and discriminant analysis of principal components revealed that 482 potato accessions could be divided into two main subpopulations. Accessions of subpopulation 1 mainly belonged to cultivars and breeding lines. Accessions of subpopulations 2 basically corresponded to wild relatives of potatoes. Results of this study provide useful information for potato improvement and conservation programs, although further studies are needed for a more accurate evaluation of genetic diversity and phenotypic traits of potatoes.
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Affiliation(s)
- Kyung-Jun Lee
- National Agrobiodiversity Center, National Institute of Agricultural Sciences (NAS), RDA, Jeonju 54874, Jeol-labuk-do, Korea; (K.-J.L.); (R.S.); (G.-T.C.); (M.Y.); (G.-A.L.)
- Honam National Institute of Biological Resources, 99, Gohadoan-gil, Mokpo-si 58762, Jeollanam-do, Korea
| | - Raveendar Sebastin
- National Agrobiodiversity Center, National Institute of Agricultural Sciences (NAS), RDA, Jeonju 54874, Jeol-labuk-do, Korea; (K.-J.L.); (R.S.); (G.-T.C.); (M.Y.); (G.-A.L.)
| | - Gyu-Taek Cho
- National Agrobiodiversity Center, National Institute of Agricultural Sciences (NAS), RDA, Jeonju 54874, Jeol-labuk-do, Korea; (K.-J.L.); (R.S.); (G.-T.C.); (M.Y.); (G.-A.L.)
| | - Munsup Yoon
- National Agrobiodiversity Center, National Institute of Agricultural Sciences (NAS), RDA, Jeonju 54874, Jeol-labuk-do, Korea; (K.-J.L.); (R.S.); (G.-T.C.); (M.Y.); (G.-A.L.)
| | - Gi-An Lee
- National Agrobiodiversity Center, National Institute of Agricultural Sciences (NAS), RDA, Jeonju 54874, Jeol-labuk-do, Korea; (K.-J.L.); (R.S.); (G.-T.C.); (M.Y.); (G.-A.L.)
| | - Do-Yoon Hyun
- National Agrobiodiversity Center, National Institute of Agricultural Sciences (NAS), RDA, Jeonju 54874, Jeol-labuk-do, Korea; (K.-J.L.); (R.S.); (G.-T.C.); (M.Y.); (G.-A.L.)
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18
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Yousaf MF, Demirel U, Naeem M, Çalışkan ME. Association mapping reveals novel genomic regions controlling some root and stolon traits in tetraploid potato ( Solanum tuberosum L.). 3 Biotech 2021; 11:174. [PMID: 33927965 DOI: 10.1007/s13205-021-02727-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 03/10/2021] [Indexed: 10/21/2022] Open
Abstract
Tuber crops have measurable biological variation in root and stolon phenotyping and thus may be utilized to identify genomic regions associated with these variations. This is the first comprehensive association mapping study related to potato root and stolon traits. A diverse panel of 192 tetraploid potato (Solanum tuberosum L.) genotypes were grown in aeroponics to reveal a biologically significant variation and detection of genomic regions associated with the root and stolon traits. Phenotyping of root traits was performed by image analysis software "WinRHIZO" (a root scanning method), and stolon traits was measured manually, while SolCAP 25K potato array was used for genotyping. Significant variation was observed between the potato genotypes for root and stolon traits along with high heritabilities (0.80 in TNS to 0.95 in SL). For marker-trait associations, Q + K linear mixed model was implemented and 50 novel genomic regions were detected. Significantly associated SNPs with stolon traits were located on chr 4, chr 6, chr 7, chr 9, chr 11 and chr 12, while those linked to root traits on chr 1, chr 2, chr 3, chr 9, chr 11, and chr 12. Structure and PCA analysis grouped genotypes into four sub-populations disclosing population genetic diversity. LD decay was observed at 2.316 Mbps (r 2 = 0.29) in the population. The identified SNPs were associated with genes performing vital functions such as root signaling and signal transduction in stress environments (GT-2 factors, protein kinases SAPK2-like and protein phosphatases "StPP1"), transcriptional and post-transcriptional gene regulation (RNA-binding proteins), sucrose synthesis and transporter families (UGPase, Sus3, SuSy, and StSUT1) and PVY resistance (Ry sto). The findings of our study can be employed in future breeding programs for improvement in potato production. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02727-6.
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Berdugo-Cely JA, Martínez-Moncayo C, Lagos-Burbano TC. Genetic analysis of a potato (Solanum tuberosum L.) breeding collection for southern Colombia using Single Nucleotide Polymorphism (SNP) markers. PLoS One 2021; 16:e0248787. [PMID: 33735184 PMCID: PMC7971539 DOI: 10.1371/journal.pone.0248787] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 03/05/2021] [Indexed: 11/18/2022] Open
Abstract
Detailed knowledge on genetic parameters such as diversity, structure, and linkage disequilibrium (LD) and identification of duplicates in a germplasm bank and/or breeding collection are essential to conservation and breeding strategies in any crop. Therefore, the potato genetic breeding collection at the Universidad de Nariño in Colombia, which is made up of diploid and tetraploid genotypes in two of the more diverse genebanks in the world, was analyzed with 8303 single nucleotide polymorphisms (SNP) from SolCAP version 1. In total, 144 genotypes from this collection were analyzed identifying an 57.2% of the polymorphic markers that allowed establishing two and three subpopulations that differentiated the diploid genotypes from the tetraploids. These subpopulations had high levels of heterozygosity and linkage disequilibrium. The diversity levels were higher in the tetraploid genotypes, while the LD levels were higher in the diploid genotypes. For the tetraploids, the genotypes from Peru had greater diversity and lower linkage disequilibrium than those from Colombia, which had slightly lower diversity and higher degrees of LD. The genetic analysis identified, adjusted and/or selected diploid and tetraploid genotypes under the following characteristics: 1) errors in classification associated with the level of ploidy; 2) presence of duplicates; and 3) genotypes with broad genetic distances and potential use in controlled hybridization processes. These analyses suggested that the potato genetic breeding collection at the Universidad de Nariño has a genetic base with a potential use in breeding programs for this crop in the Department of Nariño, in southern Colombia.
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Affiliation(s)
- Jhon A. Berdugo-Cely
- Corporación Colombiana de Investigación Agropecuaria-AGROSAVIA, Centro de Investigación Turipaná, Montería, Cereté, Colombia
- * E-mail:
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20
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Velasco-Chong JR, Herrera-Calderón O, Rojas-Armas JP, Hañari-Quispe RD, Figueroa-Salvador L, Peña-Rojas G, Andía-Ayme V, Yuli-Posadas RÁ, Yepes-Perez AF, Aguilar C. TOCOSH FLOUR ( Solanum tuberosum L.): A Toxicological Assessment of Traditional Peruvian Fermented Potatoes. Foods 2020; 9:E719. [PMID: 32498434 PMCID: PMC7353511 DOI: 10.3390/foods9060719] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/28/2020] [Accepted: 05/29/2020] [Indexed: 11/17/2022] Open
Abstract
Potato tocosh is a naturally processed potato for nutritional and curative purposes from traditional Peruvian medicine. The aim of this study was to investigate the acute and sub-acute toxicity of tocosh flour (TF). For sub-acute toxicity, TF was administered orally to rats daily once a day for 28 days at doses of 1000 mg/kg body weight (BW). Animals were observed for general behaviors, mortality, body weight variations, and histological analysis. At the end of treatment, relative organ weights, histopathology, hematological and biochemical parameters were analyzed. For acute toxicity, TF was administered orally to mice at doses of 2000 and 5000 mg/kg BW at a single dose in both sexes. Body weight, mortality, and clinical signs were observed for 14 days after treatment. The results of acute toxicity showed that the median lethal dose (LD50) value of TF is higher than 2000 g/kg BW but less than 5000 mg/Kg BW in mice. Death and toxicological symptoms were not found during the treatment. For sub-acute toxicity, we found that no-observed-adverse-effect levels (NOAEL) of TF in rats up to 1000 g/kg BW. There were statistically significant differences in body weight, and relative organ weight in the stomach and brain. No differences in hematological and biochemical parameters were observed when compared with the control group. For sub-acute toxicity, histopathological studies revealed minor abnormalities in liver and kidney tissues at doses of 5000 mg/Kg. Based on these results, TF is a traditional Peruvian medicine with high safety at up to 1000 mg/kg BW for 28 days in rats.
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Affiliation(s)
- Jonas Roberto Velasco-Chong
- Academic Department of Pharmacology, Bromatology and Toxicology, Faculty of Pharmacy and Biochemistry, Universidad Nacional Mayor de San Marcos, Jr Puno 1002, Lima 15001, Peru;
| | - Oscar Herrera-Calderón
- Academic Department of Pharmacology, Bromatology and Toxicology, Faculty of Pharmacy and Biochemistry, Universidad Nacional Mayor de San Marcos, Jr Puno 1002, Lima 15001, Peru;
| | - Juan Pedro Rojas-Armas
- Department of Dynamic Sciences, Faculty of Medicine, Universidad Nacional Mayor de San Marcos, Av. Miguel Grau 755, Cercado de Lima 15001, Peru;
| | - Renán Dilton Hañari-Quispe
- Clinical Pathology Laboratory, Faculty of Veterinary Medicine and Zootechnics, Universidad Nacional del Altiplano, Av Floral 1153, Puno 21001, Peru;
| | - Linder Figueroa-Salvador
- School of Medicine, Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas, Prolongación Primavera 2390, Lima 15023, Peru;
| | - Gilmar Peña-Rojas
- Laboratory of Cellular and Molecular Biology, Biological Sciences Faculty, Universidad Nacional de San Cristóbal de Huamanga, Portal Independencia 57, Ayacucho 05003, Peru;
| | - Vidalina Andía-Ayme
- Food Microbiology Laboratory, Biological Sciences Faculty, Universidad Nacional de San Cristóbal de Huamanga, Portal Independencia 57, Ayacucho 05003, Peru;
| | | | - Andres F. Yepes-Perez
- Chemistry of Colombian Plants, Institute of Chemistry, Faculty of Exact and Natural Sciences, University of Antioquia-UdeA, Calle 70 52–21, A.A 1226, Medellin 050010, Colombia;
| | - Cristian Aguilar
- Laboratory of Pathology, Instituto Nacional Cardiovascular, Jirón Coronel Zegarra 417, Jesús María 15072, Peru;
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21
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Zia MAB, Demirel U, Nadeem MA, Çaliskan ME. Genome-wide association study identifies various loci underlying agronomic and morphological traits in diversified potato panel. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:1003-1020. [PMID: 32377049 PMCID: PMC7196606 DOI: 10.1007/s12298-020-00785-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 02/01/2020] [Accepted: 02/21/2020] [Indexed: 05/22/2023]
Abstract
Potato is one of the most important food crops all over the world. Breeding activities for this crop are mainly aimed to improve the quality and yield of tuber. However, genetic architecture of various traits contributing to the quality and yield of potato are not yet completely understood. Genome wide association studies provides a broader way to identify the genomic regions associated with various traits. Panels of 237 tetraploid potato genotypes from different countries were grown for two consecutive years 2016 and 2017 at experimental research area of Potato research center Niğde, Turkey. A genome wide association study using SolCAP 12K array was performed for various morpho-agronomic traits. Structure algorithm and neighborhood joining analysis clearly divided all genotypes into 4 clusters on the basis of their origin. For the marker trait association, Mixed Linear Model in TASSEL was performed and 36 genomic regions were found for the traits under study. The mean r2 value was found to be 0.92 and mean significant LD was 47.5% in the populations. LD patterns reflected the breeding history of potato. The findings of present study provide a framework which could be useful for future potato breeding programs to enhance the production and to reduce the challenges in the coming years to feed world's population.
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Affiliation(s)
- Muhammad Abu Bakar Zia
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Niğde Ömer Halisdemir University, 51240 Niğde, Turkey
- College of Agriculture, Bolu Abant Izzet Baysal University, Bahadur Sub Campus Layyah, Pakistan
| | - Ufuk Demirel
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Niğde Ömer Halisdemir University, 51240 Niğde, Turkey
| | - Muhammad Azhar Nadeem
- Department of Field Crops, Faculty of Agricultural and Natural Science, Bahauddin Zakariya University, 14000 Bolu, Turkey
| | - Mehmet Emin Çaliskan
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Niğde Ömer Halisdemir University, 51240 Niğde, Turkey
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Yang X, Luo Z, Todd J, Sood S, Wang J. Genome-wide association study of multiple yield traits in a diversity panel of polyploid sugarcane (Saccharum spp.). THE PLANT GENOME 2020; 13:e20006. [PMID: 33016641 DOI: 10.1002/tpg2.20006] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 12/12/2019] [Indexed: 06/11/2023]
Abstract
Sugarcane (Saccharum spp.) is an important economic crop, contributing up to 80% of sugar and approximately 60% of biofuel globally. To meet the increased demand for sugar and biofuel supplies, it is critical to breed sugarcane cultivars with robust performance in yield traits. Therefore, dissection of causal DNA sequence variants is of great importance, as it provides genetic resources and fundamental information for crop improvement. In this study, we analyzed nine yield traits in a sugarcane diversity panel consisting of 308 accessions primarily selected from the World Collection of Sugarcane and Related Grasses. By genotyping the diversity panel via target enrichment sequencing, we identified a large number of sequence variants. Genome-wide association studies between the markers and traits were conducted, taking dosages and gene actions into consideration. In total, 217 nonredundant markers and 225 candidate genes were identified to be significantly associated with the yield traits, which can serve as a comprehensive genetic resource database for future gene identification, characterization, and selection for sugarcane improvement. We further investigated runs of homozygosity (ROH) in the sugarcane diversity panel. We characterized 282 ROHs and found that the occurrence of ROHs in the genome were nonrandom and probably under selection. The ROHs were associated with total weight and dry weight, and high ROHs resulted in a decrease in the two traits. This study suggests that genomic inbreeding has led to negative impacts on sugarcane yield.
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Affiliation(s)
- Xiping Yang
- Guangxi Key Lab for Sugarcane Biology, Guangxi Univ., Nanning, Guangxi, 530005, China
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA
| | - Ziliang Luo
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA
| | - James Todd
- Sugarcane Research Unit, USDA-ARS, Houma, LA, 70360, USA
| | - Sushma Sood
- Sugarcane Field Station, USDA, ARS, Canal Point, FL, 33438, USA
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA
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23
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Varré JS, D'Agostino N, Touzet P, Gallina S, Tamburino R, Cantarella C, Ubrig E, Cardi T, Drouard L, Gualberto JM, Scotti N. Complete Sequence, Multichromosomal Architecture and Transcriptome Analysis of the Solanum tuberosum Mitochondrial Genome. Int J Mol Sci 2019; 20:E4788. [PMID: 31561566 PMCID: PMC6801519 DOI: 10.3390/ijms20194788] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/19/2019] [Accepted: 09/24/2019] [Indexed: 12/01/2022] Open
Abstract
Mitochondrial genomes (mitogenomes) in higher plants can induce cytoplasmic male sterility and be somehow involved in nuclear-cytoplasmic interactions affecting plant growth and agronomic performance. They are larger and more complex than in other eukaryotes, due to their recombinogenic nature. For most plants, the mitochondrial DNA (mtDNA) can be represented as a single circular chromosome, the so-called master molecule, which includes repeated sequences that recombine frequently, generating sub-genomic molecules in various proportions. Based on the relevance of the potato crop worldwide, herewith we report the complete mtDNA sequence of two S. tuberosum cultivars, namely Cicero and Désirée, and a comprehensive study of its expression, based on high-coverage RNA sequencing data. We found that the potato mitogenome has a multi-partite architecture, divided in at least three independent molecules that according to our data should behave as autonomous chromosomes. Inter-cultivar variability was null, while comparative analyses with other species of the Solanaceae family allowed the investigation of the evolutionary history of their mitogenomes. The RNA-seq data revealed peculiarities in transcriptional and post-transcriptional processing of mRNAs. These included co-transcription of genes with open reading frames that are probably expressed, methylation of an rRNA at a position that should impact translation efficiency and extensive RNA editing, with a high proportion of partial editing implying frequent mis-targeting by the editing machinery.
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Affiliation(s)
- Jean-Stéphane Varré
- Univ. Lille, CNRS, Centrale Lille, UMR 9189-CRIStAL-Centre de Recherche en Informatique Signal et Automatique de Lille, F-59000 Lille, France.
| | - Nunzio D'Agostino
- CREA Research Centre for Vegetable and Ornamental Crops, 84098 Pontecagnano Faiano, SA, Italy.
| | - Pascal Touzet
- Univ. Lille, CNRS, UMR 8198-Evo-Eco-Paleo, F-59000 Lille, France.
| | - Sophie Gallina
- Univ. Lille, CNRS, UMR 8198-Evo-Eco-Paleo, F-59000 Lille, France.
| | - Rachele Tamburino
- CNR-IBBR, National Research Council of Italy, Institute of Biosciences and BioResources, 80055 Portici, NA, Italy.
| | - Concita Cantarella
- CREA Research Centre for Vegetable and Ornamental Crops, 84098 Pontecagnano Faiano, SA, Italy.
| | - Elodie Ubrig
- Institut de Biologie Moléculaire des Plantes-CNRS, Université de Strasbourg, Strasbourg 67084, France.
| | - Teodoro Cardi
- CREA Research Centre for Vegetable and Ornamental Crops, 84098 Pontecagnano Faiano, SA, Italy.
| | - Laurence Drouard
- Institut de Biologie Moléculaire des Plantes-CNRS, Université de Strasbourg, Strasbourg 67084, France.
| | - José Manuel Gualberto
- Institut de Biologie Moléculaire des Plantes-CNRS, Université de Strasbourg, Strasbourg 67084, France.
| | - Nunzia Scotti
- CNR-IBBR, National Research Council of Italy, Institute of Biosciences and BioResources, 80055 Portici, NA, Italy.
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24
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Wang Y, Rashid MAR, Li X, Yao C, Lu L, Bai J, Li Y, Xu N, Yang Q, Zhang L, Bryan GJ, Sui Q, Pan Z. Collection and Evaluation of Genetic Diversity and Population Structure of Potato Landraces and Varieties in China. FRONTIERS IN PLANT SCIENCE 2019; 10:139. [PMID: 30846993 PMCID: PMC6393402 DOI: 10.3389/fpls.2019.00139] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 01/28/2019] [Indexed: 05/26/2023]
Abstract
China is the world's leading country for potato production but potato is not native to China. To gain insights into the genetic diversity of potato germplasm various studies have been performed but no study has been reported for potato landraces in China. To improve the available genepool for future potato breeding programs, a diverse population containing 292 genotypes (including foreign elite lines, local landraces and cultivars) was developed and genotyped using 30 SSR markers covering the entire potato genome. A total of 174 alleles were detected with an average of 5.5 alleles per locus. The model-based structure analysis discriminated the population into two main sub-groups, which can be further subdivided into seven groups based on collection sites. One sub-group (P1) revealed less genetic diversity than other (P2) and contained a higher number of commercial cultivars possibly indicating a slight reduction in diversity due to selection in breeding programs. The P2 sub-group showed a wider range of genetic diversity with more new and unique alleles attained from wild relatives. The potato landraces, clustered in sub-population P1 may be derived from historical population imported from ancient European and International Potato Center genotypes while sub-population P2 may be derived from modern populations from International Potato Center and European genotypes. It is proposed that in the first step, the potato genotypes were introduced from Europe to China, domesticated as landraces, and then hybridized for modern cultivars.
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Affiliation(s)
- Ying Wang
- Industrial Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Muhammad Abdul Rehman Rashid
- Industrial Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
- Plant Breeding and Genetics, University of Agriculture Faisalabad, Burewala, Pakistan
| | - Xianping Li
- Industrial Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Chunguang Yao
- Industrial Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Lili Lu
- Industrial Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Jianming Bai
- Industrial Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Yanshan Li
- Industrial Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Ningsheng Xu
- Industrial Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Qiongfen Yang
- Industrial Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Linhai Zhang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | | | - Qijun Sui
- Industrial Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
- Scientific Observing and Experimental Station of Potato and Rapeseed in Yunnan-Guizhou Plateau, Ministry of Agriculture, Kunming, China
| | - Zhechao Pan
- Industrial Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
- Scientific Observing and Experimental Station of Potato and Rapeseed in Yunnan-Guizhou Plateau, Ministry of Agriculture, Kunming, China
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25
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Mouzo D, López-Pedrouso M, Bernal J, García L, Franco D, Zapata C. Association of Patatin-Based Proteomic Distances with Potato ( Solanum tuberosum L.) Quality Traits. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:11864-11872. [PMID: 30350976 DOI: 10.1021/acs.jafc.8b03203] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Patatin is the major tuber storage protein constituted by multiple isoforms highly variable across potato ( S. tuberosum) varieties. Here, we report a first association study of the variability of patatin isoforms between cultivars with their differences in tuber quality traits. Patatin-based proteomic distances were assessed between 15 table and/or processing potato cultivars from profiles of patatin obtained by two-dimensional electrophoresis. The content of ash, dry matter, reducing sugars, starch, total protein, and amino acid composition was also evaluated in tubers of each cultivar. Results showed that proteomic distances were significantly ( P < 0.05) associated with differences in the content of ash, dry matter, and essential amino acids. Proteomic distances were also able to identify outlier cultivars regarding the content of dry matter, content of protein, and protein quality. In conclusion, patatin-based proteomic distances can shorten the screening and selection processes of potato cultivars with advantageous characteristics in molecular breeding.
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Affiliation(s)
- Daniel Mouzo
- Department of Zoology, Genetics and Physical Anthropology , University of Santiago de Compostela , Santiago de Compostela 15782 , Spain
| | - María López-Pedrouso
- Department of Zoology, Genetics and Physical Anthropology , University of Santiago de Compostela , Santiago de Compostela 15782 , Spain
| | - Javier Bernal
- Department of Zoology, Genetics and Physical Anthropology , University of Santiago de Compostela , Santiago de Compostela 15782 , Spain
| | - Lucio García
- Meat Technology Center of Galicia, r/Galicia 4 , Parque Tecnolóxico de Galicia , San Cibrao das Viñas , Ourense 32900 , Spain
| | - Daniel Franco
- Meat Technology Center of Galicia, r/Galicia 4 , Parque Tecnolóxico de Galicia , San Cibrao das Viñas , Ourense 32900 , Spain
| | - Carlos Zapata
- Department of Zoology, Genetics and Physical Anthropology , University of Santiago de Compostela , Santiago de Compostela 15782 , Spain
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26
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Sharma SK, MacKenzie K, McLean K, Dale F, Daniels S, Bryan GJ. Linkage Disequilibrium and Evaluation of Genome-Wide Association Mapping Models in Tetraploid Potato. G3 (BETHESDA, MD.) 2018; 8:3185-3202. [PMID: 30082329 PMCID: PMC6169395 DOI: 10.1534/g3.118.200377] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 07/30/2018] [Indexed: 11/18/2022]
Abstract
Genome-wide association studies (GWAS) have become a powerful tool for analyzing complex traits in crop plants. The current study evaluates the efficacy of various GWAS models and methods for elucidating population structure in potato. The presence of significant population structure can lead to detection of spurious marker-trait associations, as well as mask true ones. While appropriate statistical models are needed to detect true marker-trait associations, in most published potato GWAS, a 'one model fits all traits' approach has been adopted. We have examined various GWAS models on a large association panel comprising diverse tetraploid potato cultivars and breeding lines, genotyped with single nucleotide polymorphism (SNP) markers. Phenotypic data were generated for 20 quantitative traits assessed in different environments. Best Linear Unbiased Estimates (BLUEs) for these traits were obtained for use in assessing GWAS models. Goodness of fit of GWAS models, derived using different combinations of kinship and population structure for all traits, was evaluated using Quantile-Quantile (Q-Q) plots and genomic control inflation factors (λGC). Kinship was found to play a major role in correcting population confounding effects and results advocate a 'trait-specific' fit of different GWAS models. A survey of genome-wide linkage disequilibrium (LD), one of the critical factors affecting GWAS, is also presented and our findings are compared to other recent studies in potato. The genetic material used here, and the outputs of this study represent a novel resource for genetic analysis in potato.
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Affiliation(s)
| | - Katrin MacKenzie
- Biomathematics and Statistics Scotland (BioSS), Dundee DD2 5DA, UK
| | | | - Finlay Dale
- The James Hutton Institute, Dundee DD2 5DA, UK
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27
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Santa JD, Berdugo-Cely J, Cely-Pardo L, Soto-Suárez M, Mosquera T, Galeano M. CH. QTL analysis reveals quantitative resistant loci for Phytophthora infestans and Tecia solanivora in tetraploid potato (Solanum tuberosum L.). PLoS One 2018; 13:e0199716. [PMID: 29979690 PMCID: PMC6034811 DOI: 10.1371/journal.pone.0199716] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 06/12/2018] [Indexed: 11/18/2022] Open
Abstract
Late blight and Guatemalan potato tuber moth caused by Phytophthora infestans and Tecia solanivora, respectively, are major phytosanitary problems on potato crops in Colombia and Ecuador. Hence, the development of resistant cultivars is an alternative for their control. However, breeding initiatives for durable resistance using molecular tools are limited due to the genome complexity and high heterozygosity in autotetraploid potatoes. To contribute to a better understanding of the genetic basis underlying the resistance to P. infestans and T. solanivora in potato, the aim of this study was to identify QTLs for resistance to P. infestans and T. solanivora using a F1 tetraploid potato segregant population for both traits. Ninety-four individuals comprised this population. Parent genotypes and their progeny were genotyped using SOLCAP 12K potato array. Forty-five percent of the markers were polymorphic. A genetic linkage map was built with a length of 968.4 cM and 1,287 SNPs showing good distribution across the genome. Severity and incidence were evaluated in two crop cycles for two years. QTL analysis revealed six QTLs linked to P. infestans, four of these related to previous QTLs reported, and two novel QTLs (qrAUDPC-3 and qrAUDPC-8). Fifteen QTLs were linked to T. solanivora, being qIPC-6 and qOPA-6.1, and qIPC-10 and qIPC-10.1 stable in two different trials. This study is one of the first to identify QTLs for T. solanivora. As the population employed is a breeding population, results will contribute significantly to breeding programs to select resistant plant material, especially in countries where P. infestans and T. solanivora limit potato production.
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Affiliation(s)
- Juan David Santa
- Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA), C.I. Tibaitatá, Cundinamarca, Colombia
- Faculty of Agricultural Sciences, Universidad Nacional de Colombia, sede Bogotá, Colombia
| | - Jhon Berdugo-Cely
- Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA), C.I. Tibaitatá, Cundinamarca, Colombia
| | - Liliana Cely-Pardo
- Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA), C.I. Tibaitatá, Cundinamarca, Colombia
| | - Mauricio Soto-Suárez
- Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA), C.I. Tibaitatá, Cundinamarca, Colombia
| | - Teresa Mosquera
- Faculty of Agricultural Sciences, Universidad Nacional de Colombia, sede Bogotá, Colombia
| | - Carlos H. Galeano M.
- Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA), C.I. Palmira, Valle del Cauca, Colombia
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28
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Bastien M, Boudhrioua C, Fortin G, Belzile F. Exploring the potential and limitations of genotyping-by-sequencing for SNP discovery and genotyping in tetraploid potato. Genome 2018; 61:449-456. [PMID: 29688035 DOI: 10.1139/gen-2017-0236] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Genotyping-by-sequencing (GBS) potentially offers a cost-effective alternative for SNP discovery and genotyping. Here, we report the exploration of GBS in tetraploid potato. Both ApeKI and PstI/MspI enzymes were used for library preparation on eight diverse potato genotypes. ApeKI yielded more markers than PstI/MspI but provided a lower read coverage per marker, resulting in more missing data and limiting effective genotyping to the tetraploid mode. We then assessed the accuracy of these SNPs by comparison with SolCAP data (5824 data points in diploid mode and 3243 data points in tetraploid mode) and found the match rates between genotype calls was 90.4% and 81.3%, respectively. Imputation of missing data did not prove very accurate because of incomplete haplotype discovery, suggesting caution in setting the allowance for missing data. To further assess the quality of GBS-derived data, a genome-wide association analysis was performed for flower color on 318 clones (with ApeKI). A strong association signal on chromosome 2 was obtained with the most significant SNP located in the middle of the dihydroflavonol 4-reductase (DFR) gene. We conclude that an appropriate choice of enzyme for GBS library preparation makes it possible to obtain high-quality SNPs in potato and will be helpful for marker-assisted genomics.
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Affiliation(s)
- Maxime Bastien
- Département de phytologie and Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Quebec City, QC G1V 0A6, Canada.,Département de phytologie and Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Chiheb Boudhrioua
- Département de phytologie and Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Quebec City, QC G1V 0A6, Canada.,Département de phytologie and Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Gabrielle Fortin
- Département de phytologie and Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Quebec City, QC G1V 0A6, Canada.,Département de phytologie and Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Quebec City, QC G1V 0A6, Canada
| | - François Belzile
- Département de phytologie and Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Quebec City, QC G1V 0A6, Canada
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29
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Deperi SI, Tagliotti ME, Bedogni MC, Manrique-Carpintero NC, Coombs J, Zhang R, Douches D, Huarte MA. Discriminant analysis of principal components and pedigree assessment of genetic diversity and population structure in a tetraploid potato panel using SNPs. PLoS One 2018; 13:e0194398. [PMID: 29547652 PMCID: PMC5856401 DOI: 10.1371/journal.pone.0194398] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 03/03/2018] [Indexed: 12/03/2022] Open
Abstract
The reported narrow genetic base of cultivated potato (Solanum tuberosum) can be expanded by the introgression of many related species with large genetic diversity. The analysis of the genetic structure of a potato population is important to broaden the genetic base of breeding programs by the identification of different genetic pools. A panel composed by 231 diverse genotypes was characterized using single nucleotide polymorphism (SNP) markers of the Illumina Infinium Potato SNP Array V2 to identify population structure and assess genetic diversity using discriminant analysis of principal components (DAPC) and pedigree analysis. Results revealed the presence of five clusters within the populations differentiated principally by ploidy, taxonomy, origin and breeding program. The information obtained in this work could be readily used as a guide for parental introduction in new breeding programs that want to maximize variability by combination of contrasting variability sources such as those presented here.
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Affiliation(s)
- Sofía. I. Deperi
- National Research Council of Argentina (CONICET), Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
- * E-mail: (SID); (MAH)
| | - Martín. E. Tagliotti
- National Research Council of Argentina (CONICET), Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - M. Cecilia Bedogni
- National Institute for Agricultural Technology (INTA), EEA INTA Balcarce, Balcarce, Buenos Aires, Argentina
| | | | - Joseph Coombs
- Michigan State University, East Lansing, Michigan, United States
| | - Ruofang Zhang
- Inner Mongolia University, Hohhot, Inner Mongolia, China
| | - David Douches
- Michigan State University, East Lansing, Michigan, United States
| | - Marcelo. A. Huarte
- National Institute for Agricultural Technology (INTA), EEA INTA Balcarce, Balcarce, Buenos Aires, Argentina
- * E-mail: (SID); (MAH)
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30
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Bali S, Robinson BR, Sathuvalli V, Bamberg J, Goyer A. Single Nucleotide Polymorphism (SNP) markers associated with high folate content in wild potato species. PLoS One 2018; 13:e0193415. [PMID: 29474475 PMCID: PMC5825101 DOI: 10.1371/journal.pone.0193415] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 02/09/2018] [Indexed: 11/23/2022] Open
Abstract
Micronutrient deficiency, also known as the hidden hunger, affects over two billion people worldwide. Potato is the third most consumed food crops in the world, and is therefore a fundamental element of food security for millions of people. Increasing the amount of micronutrients in food crop could help alleviate worldwide micronutrient malnutrition. In the present study, we report on the identification of single nucleotide polymorphism (SNP) markers associated with folate, an essential micronutrient in the human diet. A high folate diploid clone Fol 1.6 from the wild potato relative Solanum boliviense (PI 597736) was crossed with a low/medium folate diploid S. tuberosum clone USW4self#3. The resulting F1 progeny was intermated to generate an F2 population, and tubers from 94 F2 individuals were harvested for folate analysis and SNP genotyping using a SolCap 12K Potato SNP array. Folate content in the progeny ranged from 304 to 2,952 ng g-1 dry weight. 6,759 high quality SNPs containing 4,174 (62%) polymorphic and 2,585 (38%) monomorphic SNPs were used to investigate marker-trait association. Association analysis was performed using two different approaches: survey SNP-trait association (SSTA) and SNP-trait association (STA). A total of 497 significant SNPs were identified, 489 by SSTA analysis and 43 by STA analysis. Markers identified by SSTA were located on all twelve chromosomes while those identified by STA were confined to chromosomes 2, 4, and 6. Eighteen of the significant SNPs were located within or in close proximity to folate metabolism-related genes. Forty two SNPs were identical between SSTA and STA analyses. These SNPs have potential to be used in marker-assisted selection for breeding high folate potato varieties.
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Affiliation(s)
- Sapinder Bali
- Hermiston Agricultural Research and Extension Center, Oregon State University, Hermiston, OR, United States of America
| | - Bruce R. Robinson
- Hermiston Agricultural Research and Extension Center, Oregon State University, Hermiston, OR, United States of America
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, United States of America
| | - Vidyasagar Sathuvalli
- Hermiston Agricultural Research and Extension Center, Oregon State University, Hermiston, OR, United States of America
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, United States of America
| | - John Bamberg
- USDA/Agricultural Research Service, US Potato Genebank, Sturgeon Bay, WI, United States of America
| | - Aymeric Goyer
- Hermiston Agricultural Research and Extension Center, Oregon State University, Hermiston, OR, United States of America
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States of America
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31
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McElroy MS, Navarro AJR, Mustiga G, Stack C, Gezan S, Peña G, Sarabia W, Saquicela D, Sotomayor I, Douglas GM, Migicovsky Z, Amores F, Tarqui O, Myles S, Motamayor JC. Prediction of Cacao ( Theobroma cacao) Resistance to Moniliophthora spp. Diseases via Genome-Wide Association Analysis and Genomic Selection. FRONTIERS IN PLANT SCIENCE 2018; 9:343. [PMID: 29662497 PMCID: PMC5890178 DOI: 10.3389/fpls.2018.00343] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Accepted: 02/28/2018] [Indexed: 05/21/2023]
Abstract
Cacao (Theobroma cacao) is a globally important crop, and its yield is severely restricted by disease. Two of the most damaging diseases, witches' broom disease (WBD) and frosty pod rot disease (FPRD), are caused by a pair of related fungi: Moniliophthora perniciosa and Moniliophthora roreri, respectively. Resistant cultivars are the most effective long-term strategy to address Moniliophthora diseases, but efficiently generating resistant and productive new cultivars will require robust methods for screening germplasm before field testing. Marker-assisted selection (MAS) and genomic selection (GS) provide two potential avenues for predicting the performance of new genotypes, potentially increasing the selection gain per unit time. To test the effectiveness of these two approaches, we performed a genome-wide association study (GWAS) and GS on three related populations of cacao in Ecuador genotyped with a 15K single nucleotide polymorphism (SNP) microarray for three measures of WBD infection (vegetative broom, cushion broom, and chirimoya pod), one of FPRD (monilia pod) and two productivity traits (total fresh weight of pods and % healthy pods produced). GWAS yielded several SNPs associated with disease resistance in each population, but none were significantly correlated with the same trait in other populations. Genomic selection, using one population as a training set to estimate the phenotypes of the remaining two (composed of different families), varied among traits, from a mean prediction accuracy of 0.46 (vegetative broom) to 0.15 (monilia pod), and varied between training populations. Simulations demonstrated that selecting seedlings using GWAS markers alone generates no improvement over selecting at random, but that GS improves the selection process significantly. Our results suggest that the GWAS markers discovered here are not sufficiently predictive across diverse germplasm to be useful for MAS, but that using all markers in a GS framework holds substantial promise in accelerating disease-resistance in cacao.
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Affiliation(s)
- Michel S. McElroy
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
| | - Alberto J. R. Navarro
- MARS, Incorporated c/o United States Department of Agriculture – Agricultural Research Service, Miami, FL, United States
| | - Guiliana Mustiga
- MARS, Incorporated c/o United States Department of Agriculture – Agricultural Research Service, Miami, FL, United States
| | - Conrad Stack
- MARS, Incorporated c/o United States Department of Agriculture – Agricultural Research Service, Miami, FL, United States
| | - Salvador Gezan
- School of Forest Resources and Conservation, College of Agricultural and Life Sciences, University of Florida, Gainesville, FL, United States
| | - Geover Peña
- Instituto Nacional de Investigaciones Agropecuarias, Quito, Ecuador
| | - Widem Sarabia
- Instituto Nacional de Investigaciones Agropecuarias, Quito, Ecuador
| | - Diego Saquicela
- Instituto Nacional de Investigaciones Agropecuarias, Quito, Ecuador
| | | | - Gavin M. Douglas
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
| | - Zoë Migicovsky
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
| | - Freddy Amores
- Facultad de Ciencias Agrarias, Universidad Técnica Estatal de Quevedo, Quevedo, Ecuador
| | - Omar Tarqui
- Instituto Nacional de Investigaciones Agropecuarias, Quito, Ecuador
| | - Sean Myles
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
| | - Juan C. Motamayor
- MARS, Incorporated c/o United States Department of Agriculture – Agricultural Research Service, Miami, FL, United States
- *Correspondence: Juan C. Motamayor,
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Álvarez MF, Angarita M, Delgado MC, García C, Jiménez-Gomez J, Gebhardt C, Mosquera T. Identification of Novel Associations of Candidate Genes with Resistance to Late Blight in Solanum tuberosum Group Phureja. FRONTIERS IN PLANT SCIENCE 2017; 8:1040. [PMID: 28674545 PMCID: PMC5475386 DOI: 10.3389/fpls.2017.01040] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 05/30/2017] [Indexed: 05/16/2023]
Abstract
The genetic basis of quantitative disease resistance has been studied in crops for several decades as an alternative to R gene mediated resistance. The most important disease in the potato crop is late blight, caused by the oomycete Phytophthora infestans. Quantitative disease resistance (QDR), as any other quantitative trait in plants, can be genetically mapped to understand the genetic architecture. Association mapping using DNA-based markers has been implemented in many crops to dissect quantitative traits. We used an association mapping approach with candidate genes to identify the first genes associated with quantitative resistance to late blight in Solanum tuberosum Group Phureja. Twenty-nine candidate genes were selected from a set of genes that were differentially expressed during the resistance response to late blight in tetraploid European potato cultivars. The 29 genes were amplified and sequenced in 104 accessions of S. tuberosum Group Phureja from Latin America. We identified 238 SNPs in the selected genes and tested them for association with resistance to late blight. The phenotypic data were obtained under field conditions by determining the area under disease progress curve (AUDPC) in two seasons and in two locations. Two genes were associated with QDR to late blight, a potato homolog of thylakoid lumen 15 kDa protein (StTL15A) and a stem 28 kDa glycoprotein (StGP28). Key message: A first association mapping experiment was conducted in Solanum tuberosum Group Phureja germplasm, which identified among 29 candidates two genes associated with quantitative resistance to late blight.
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Affiliation(s)
- María F. Álvarez
- Facultad de Ciencias Agrarias, Universidad Nacional de ColombiaBogotá, Colombia
- Rice Program International Centre for Tropical Agriculture (CIAT)Cali, Colombia
| | - Myrian Angarita
- Facultad de Ciencias Agrarias, Universidad Nacional de ColombiaBogotá, Colombia
| | - María C. Delgado
- Facultad de Ciencias Agrarias, Universidad Nacional de ColombiaBogotá, Colombia
| | - Celsa García
- Facultad de Ciencias Agrarias, Universidad Nacional de ColombiaBogotá, Colombia
| | - José Jiménez-Gomez
- Department of Genetics and Plant Breeding, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | - Christiane Gebhardt
- Department of Genetics and Plant Breeding, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | - Teresa Mosquera
- Facultad de Ciencias Agrarias, Universidad Nacional de ColombiaBogotá, Colombia
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Romero AP, Alarcón A, Valbuena RI, Galeano CH. Physiological Assessment of Water Stress in Potato Using Spectral Information. FRONTIERS IN PLANT SCIENCE 2017; 8:1608. [PMID: 28979277 PMCID: PMC5611683 DOI: 10.3389/fpls.2017.01608] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 09/04/2017] [Indexed: 05/19/2023]
Abstract
Water stress in potato (Solanum tuberosum L.) causes considerable losses in yield, and therefore, potato is often considered to be a drought sensitive crop. Identification of water deficit tolerant potato genotypes is an adaptation strategy to mitigate the climatic changes that are occurring in the Cundiboyacense region in Colombia. Previous studies have evaluated potato plants under water stress conditions using physiological analyses. However, these methodologies require considerable amounts of time and plant material to perform these measurements. This study evaluated and compared the physiological and spectral traits between two genotypes, Diacol Capiro and Perla Negra under two drought levels (10 and 15 days without irrigation from flowering). Reflectance information was used to calculate indexes which were associated with the physiological behavior in plants. The results showed that spectral information was correlated (ρ < 0.0001) with physiological variables such as foliar area (FA), total water content (H2Ot), relative growth rate of potato tubers (RGTtub), leaf area ratio (LAR), and foliar area index (AFI). In general, there was a higher concentration of chlorophyll under drought treatments. In addition, Perla Negra under water deficit treatments did not show significant differences in its physiological variables. Therefore, it could be considered a drought tolerant genotype because its physiological performance was not affected under water stress conditions. However, yield was affected in both genotypes after being subject to 15 days of drought. The results suggested that reflectance indexes are a useful and affordable approach for potato phenotyping to select parent and segregant populations in breeding programs.
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