1
|
Osorio-Guarin JA, Higgins J, Toloza-Moreno DL, Di Palma F, Enriquez Valencia AL, Riveros Munévar F, De Vega JJ, Yockteng R. Genome-wide association analyses using multilocus models on bananas (Musa spp.) reveal candidate genes related to morphology, fruit quality, and yield. G3 (BETHESDA, MD.) 2024; 14:jkae108. [PMID: 38775627 PMCID: PMC11304972 DOI: 10.1093/g3journal/jkae108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 05/17/2024] [Indexed: 08/09/2024]
Abstract
Bananas (Musa spp.) are an essential fruit worldwide and rank as the fourth most significant food crop for addressing malnutrition due to their rich nutrients and starch content. The potential of their genetic diversity remains untapped due to limited molecular breeding tools. Our study examined a phenotypically diverse group of 124 accessions from the Colombian Musaceae Collection conserved in AGROSAVIA. We assessed 12 traits categorized into morphology, fruit quality, and yield, alongside sequence data. Our sequencing efforts provided valuable insights, with an average depth of about 7× per accession, resulting in 187,133 single-nucleotide polymorphisms (SNPs) against Musa acuminata (A genome) and 220,451 against Musa balbisiana (B genome). Population structure analysis grouped samples into four and five clusters based on the reference genome. By using different association models, we identified marker-trait associations (MTAs). The mixed linear model revealed four MTAs, while the Bayesian-information and linkage-disequilibrium iteratively nested keyway and fixed and random model for circulating probability unification models identified 82 and 70 MTAs, respectively. We identified 38 and 40 candidate genes in linkage proximity to significant MTAs for the A genome and B genome, respectively. Our findings provide insights into the genetic underpinnings of morphology, fruit quality, and yield. Once validated, the SNP markers and candidate genes can potentially drive advancements in genomic-guided breeding strategies to enhance banana crop improvement.
Collapse
Affiliation(s)
- Jaime Andrés Osorio-Guarin
- Centro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria, AGROSAVIA, Km 14 vía Mosquera, Cundinamarca 250047, Colombia
| | - Janet Higgins
- Earlham Institute, Norwich Research Park, NR4 7UZ Norwich, UK
| | - Deisy Lisseth Toloza-Moreno
- Centro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria, AGROSAVIA, Km 14 vía Mosquera, Cundinamarca 250047, Colombia
| | | | - Ayda Lilia Enriquez Valencia
- Centro de Investigación Palmira, Corporación Colombiana de Investigación Agropecuaria, AGROSAVIA, Palmira, Valle del Cauca 763533, Colombia
| | - Fernando Riveros Munévar
- Facultad de Psicología y Ciencias del Comportamiento, Universidad de La Sabana, Chía, Cundinamarca 250001, Colombia
| | - José J De Vega
- Earlham Institute, Norwich Research Park, NR4 7UZ Norwich, UK
| | - Roxana Yockteng
- Centro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria, AGROSAVIA, Km 14 vía Mosquera, Cundinamarca 250047, Colombia
- Institut de Systématique, Evolution, Biodiversité-UMR-CNRS 7205, Muséum National d´Histoire Naturelle, Paris, Ile 75005, France
| |
Collapse
|
2
|
Wang X, Liu Z, Zhang F, Xiao H, Cao S, Xue H, Liu W, Su Y, Liu Z, Zhong H, Zhang F, Ahmad B, Long Q, Zhang Y, Liu Y, Gan Y, Hou T, Jin Z, Wu X, Liu G, Wang Y, Peng Y, Zhou Y. Integrative genomics reveals the polygenic basis of seedlessness in grapevine. Curr Biol 2024:S0960-9822(24)00925-4. [PMID: 39094571 DOI: 10.1016/j.cub.2024.07.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 05/04/2024] [Accepted: 07/03/2024] [Indexed: 08/04/2024]
Abstract
Seedlessness is a crucial quality trait in table grape (Vitis vinifera L.) breeding. However, the development of seeds involved intricate regulations, and the polygenic basis of seed abortion remains unclear. Here, we combine comparative genomics, population genetics, quantitative genetics, and integrative genomics to unravel the evolution and polygenic basis of seedlessness in grapes. We generated the haplotype-resolved genomes for two seedless grape cultivars, "Thompson Seedless" (TS, syn. "Sultania") and "Black Monukka" (BM). Comparative genomics identified a ∼4.25 Mb hemizygous inversion on Chr10 specific in seedless cultivars, with seedless-associated genes VvTT16 and VvSUS2 located at breakpoints. Population genomic analyses of 548 grapevine accessions revealed two distinct clusters of seedless cultivars, and the identity-by-descent (IBD) results indicated that the origin of the seedlessness trait could be traced back to "Sultania." Introgression, rather than convergent selection, shaped the evolutionary history of seedlessness in grape improvement. Genome-wide association study (GWAS) analysis identified 110 quantitative trait loci (QTLs) associated with 634 candidate genes, including previously unidentified candidate genes, such as three 11S GLOBULIN SEED STORAGE PROTEIN and two CYTOCHROME P450 genes, and well-known genes like VviAGL11. Integrative genomic analyses resulted in 339 core candidate genes categorized into 13 functional categories related to seed development. Machine learning-based genomic selection achieved a remarkable prediction accuracy of 97% for seedlessness in grapevines. Our findings highlight the polygenic nature of seedlessness and provide candidate genes for molecular genetics and an effective prediction for seedlessness in grape genomic breeding.
Collapse
Affiliation(s)
- Xu Wang
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China; School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, Ireland
| | - Zhongjie Liu
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Fan Zhang
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Hua Xiao
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Shuo Cao
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Hui Xue
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Wenwen Liu
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Ying Su
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhenya Liu
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Haixia Zhong
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Fuchun Zhang
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Bilal Ahmad
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Qiming Long
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yingchun Zhang
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yuting Liu
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yu Gan
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Ting Hou
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhongxin Jin
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xinyu Wu
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Guotian Liu
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yiwen Wang
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yanling Peng
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yongfeng Zhou
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China; National Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.
| |
Collapse
|
3
|
Yan L, Song W, Wang Z, Yu D, Sudini H, Kang Y, Lei Y, Huai D, Chen Y, Wang X, Wang Q, Liao B. Dissection of the Genetic Basis of Resistance to Stem Rot in Cultivated Peanuts ( Arachis hypogaea L.) through Genome-Wide Association Study. Genes (Basel) 2023; 14:1447. [PMID: 37510351 PMCID: PMC10378806 DOI: 10.3390/genes14071447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 07/09/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Peanut (Arachis hypogaea) is an important oilseed and cash crop worldwide, contributing an important source of edible oil and protein for human nutrition. However, the incidence of stem rot disease caused by Athelia rolfsii poses a major challenge to peanut cultivation, resulting in significant yield losses. In this study, a panel of 202 peanut accessions was evaluated for their resistance to stem rot by inoculating plants in the field with A. rolfsii-infested oat grains in three environments. The mean disease index value of each environment for accessions in subsp. fasitigiate and subsp. hypogaea showed no significant difference. Accessions from southern China displayed the lowest disease index value compared to those from other ecological regions. We used whole-genome resequencing to analyze the genotypes of the accessions and to identify significant SNPs associated with stem rot resistance through genome-wide association study (GWAS). A total of 121 significant SNPs associated with stem rot resistance in peanut were identified, with phenotypic variation explained (PVE) ranging from 12.23% to 15.51%. A total of 27 candidate genes within 100 kb upstream and downstream of 23 significant SNPs were annotated, which have functions related to recognition, signal transduction, and defense response. These significant SNPs and candidate genes provide valuable information for further validation and molecular breeding to improve stem rot resistance in peanut.
Collapse
Affiliation(s)
- Liying Yan
- Key Laboratory of Oil Crops Biology and Genetic Improvement, Ministry of Agricultural and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Wanduo Song
- Key Laboratory of Oil Crops Biology and Genetic Improvement, Ministry of Agricultural and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Zhihui Wang
- Key Laboratory of Oil Crops Biology and Genetic Improvement, Ministry of Agricultural and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Dongyang Yu
- Key Laboratory of Oil Crops Biology and Genetic Improvement, Ministry of Agricultural and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Hari Sudini
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, India
| | - Yanping Kang
- Key Laboratory of Oil Crops Biology and Genetic Improvement, Ministry of Agricultural and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Yong Lei
- Key Laboratory of Oil Crops Biology and Genetic Improvement, Ministry of Agricultural and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Dongxin Huai
- Key Laboratory of Oil Crops Biology and Genetic Improvement, Ministry of Agricultural and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Yuning Chen
- Key Laboratory of Oil Crops Biology and Genetic Improvement, Ministry of Agricultural and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Xin Wang
- Key Laboratory of Oil Crops Biology and Genetic Improvement, Ministry of Agricultural and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Qianqian Wang
- Key Laboratory of Oil Crops Biology and Genetic Improvement, Ministry of Agricultural and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Boshou Liao
- Key Laboratory of Oil Crops Biology and Genetic Improvement, Ministry of Agricultural and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| |
Collapse
|
4
|
Chen A, Sun J, Viljoen A, Mostert D, Xie Y, Mangila L, Bothma S, Lyons R, Hřibová E, Christelová P, Uwimana B, Amah D, Pearce S, Chen N, Batley J, Edwards D, Doležel J, Crisp P, Brown AF, Martin G, Yahiaoui N, D'Hont A, Coin L, Swennen R, Aitken EAB. Genetic Mapping, Candidate Gene Identification and Marker Validation for Host Plant Resistance to the Race 4 of Fusarium oxysporum f. sp. cubense Using Musa acuminata ssp. malaccensis. Pathogens 2023; 12:820. [PMID: 37375510 DOI: 10.3390/pathogens12060820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/04/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
Fusarium wilt of banana is a devastating disease that has decimated banana production worldwide. Host resistance to Fusarium oxysporum f. sp. Cubense (Foc), the causal agent of this disease, is genetically dissected in this study using two Musa acuminata ssp. Malaccensis segregating populations, segregating for Foc Tropical (TR4) and Subtropical (STR4) race 4 resistance. Marker loci and trait association using 11 SNP-based PCR markers allowed the candidate region to be delimited to a 12.9 cM genetic interval corresponding to a 959 kb region on chromosome 3 of 'DH-Pahang' reference assembly v4. Within this region, there was a cluster of pattern recognition receptors, namely leucine-rich repeat ectodomain containing receptor-like protein kinases, cysteine-rich cell-wall-associated protein kinases, and leaf rust 10 disease-resistance locus receptor-like proteins, positioned in an interspersed arrangement. Their transcript levels were rapidly upregulated in the resistant progenies but not in the susceptible F2 progenies at the onset of infection. This suggests that one or several of these genes may control resistance at this locus. To confirm the segregation of single-gene resistance, we generated an inter-cross between the resistant parent 'Ma850' and a susceptible line 'Ma848', to show that the STR4 resistance co-segregated with marker '28820' at this locus. Finally, an informative SNP marker 29730 allowed the locus-specific resistance to be assessed in a collection of diploid and polyploid banana plants. Of the 60 lines screened, 22 lines were predicted to carry resistance at this locus, including lines known to be TR4-resistant, such as 'Pahang', 'SH-3362', 'SH-3217', 'Ma-ITC0250', and 'DH-Pahang/CIRAD 930'. Additional screening in the International Institute for Tropical Agriculture's collection suggests that the dominant allele is common among the elite 'Matooke' NARITA hybrids, as well as in other triploid or tetraploid hybrids derived from East African highland bananas. Fine mapping and candidate gene identification will allow characterization of molecular mechanisms underlying the TR4 resistance. The markers developed in this study can now aid the marker-assisted selection of TR4 resistance in breeding programs around the world.
Collapse
Affiliation(s)
- Andrew Chen
- School of Agriculture and Food Science, The University of Queensland, Brisbane, QLD 4067, Australia
| | - Jiaman Sun
- School of Agriculture and Food Science, The University of Queensland, Brisbane, QLD 4067, Australia
- School of Life Science, Jiaying University, Meizhou 514015, China
| | - Altus Viljoen
- Department of Plant Pathology, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Diane Mostert
- Department of Plant Pathology, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Yucong Xie
- Department of Biology, Duke University, Durham, NC 27708-0338, USA
| | - Leroy Mangila
- School of Agriculture and Food Science, The University of Queensland, Brisbane, QLD 4067, Australia
| | - Sheryl Bothma
- Department of Plant Pathology, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Rebecca Lyons
- School of Agriculture and Food Science, The University of Queensland, Brisbane, QLD 4067, Australia
| | - Eva Hřibová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Bio-Technological and Agricultural Research, CZ-77900 Olomouc, Czech Republic
| | - Pavla Christelová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Bio-Technological and Agricultural Research, CZ-77900 Olomouc, Czech Republic
| | - Brigitte Uwimana
- International Institute of Tropical Agriculture, Kampala P.O. Box 7878, Uganda
| | - Delphine Amah
- International Institute of Tropical Agriculture, Ibadan PMB 5320, Nigeria
| | - Stephen Pearce
- Sustainable Soils and Crops, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
| | - Ning Chen
- School of Agriculture and Food Science, The University of Queensland, Brisbane, QLD 4067, Australia
| | - Jacqueline Batley
- School of Biological Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - David Edwards
- School of Biological Sciences, The University of Western Australia, Perth, WA 6009, Australia
- The Centre for Applied Bioinformatics, University of Western Australia, Crawley, Perth, WA 6009, Australia
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Bio-Technological and Agricultural Research, CZ-77900 Olomouc, Czech Republic
| | - Peter Crisp
- School of Agriculture and Food Science, The University of Queensland, Brisbane, QLD 4067, Australia
| | - Allan F Brown
- International Institute of Tropical Agriculture, Arusha P.O. Box 447, Tanzania
| | - Guillaume Martin
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
- UMR AGAP Institut, Université de Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
| | - Nabila Yahiaoui
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
- UMR AGAP Institut, Université de Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
| | - Angelique D'Hont
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
- UMR AGAP Institut, Université de Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
| | - Lachlan Coin
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3004, Australia
| | - Rony Swennen
- International Institute of Tropical Agriculture, Kampala P.O. Box 7878, Uganda
- Division of Crop Biotechnics, Laboratory of Tropical Crop Improvement, Katholieke Universiteit Leuven, 3001 Leuven, Belgium
| | - Elizabeth A B Aitken
- School of Agriculture and Food Science, The University of Queensland, Brisbane, QLD 4067, Australia
| |
Collapse
|
5
|
Gardoce RR, Manohar ANC, Mendoza JVS, Tejano MS, Nocum JDL, Lachica GC, Gueco LS, Cueva FMD, Lantican DV. A novel SNP panel developed for targeted genotyping-by-sequencing (GBS) reveals genetic diversity and population structure of Musa spp. germplasm collection. Mol Genet Genomics 2023; 298:857-869. [PMID: 37085697 DOI: 10.1007/s00438-023-02018-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 04/08/2023] [Indexed: 04/23/2023]
Abstract
The Philippines is situated in the geographic region regarded as the center of diversity of banana and its wild relatives (Musa spp.). It holds the most extensive collection of B-genome germplasm in the world along with A-genome groups and several natural hybrids with A- and B-genome combinations. Management of this germplasm resource has relied immensely on identification using local names and morphological characters, and the extent of genetic diversity of the collection has not been achieved with molecular markers. A high-throughput and reliable genotyping method for banana and its relatives will facilitate germplasm management and support breeding initiatives toward a marker-based approach. Here, we developed a 1 K SNP genotyping panel based on filtering of high-quality genome-wide SNPs from the Musa Germplasm Information System and used it to assess the genetic diversity and population structure of 183 accessions from a Musa spp. germplasm collection containing Philippine and foreign accessions. Targeted GBS using SeqSNP™ technology generated 70,376,284 next-generation sequencing (NGS) reads with an average effective target SNP coverage of 340 × . Bioinformatics pipeline revealed 971 polymorphic SNPs containing 76.9% homozygous calls, 23.1% heterozygous calls and 4% with missing data. A final set of 952 SNPs detected 2,092 alleles. Pairwise genetic distance varied from 0.0021 to 0.3325 with most pairs of accessions distinguished with 250 to 300 loci. The SNP panel was able to detect seven (k = 7) genetically differentiated groups and its composition through Principal Component Analysis (PCA) with k-means clustering algorithm and Discriminant Analysis of Principal Components (DAPC). Accession-specific SNPs were also identified. The 1 K SNP panel effectively distinguishes between genomic groups and provides relatively good resolution of genome-wide nucleotide diversity of Musa spp. This panel is recommended for low-density genotyping for application in marker-assisted breeding and germplasm management, and could be further enhanced to increase marker density for other applications like genetic association and genomic selection in bananas.
Collapse
Affiliation(s)
- Roanne R Gardoce
- Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, 4031, Laguna, Philippines.
| | - Anand Noel C Manohar
- Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, 4031, Laguna, Philippines
| | - Jay-Vee S Mendoza
- Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, 4031, Laguna, Philippines
| | - Maila S Tejano
- Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, 4031, Laguna, Philippines
| | - Jen Daine L Nocum
- Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, 4031, Laguna, Philippines
| | - Grace C Lachica
- Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, 4031, Laguna, Philippines
- Philippine Genome Center Program for Agriculture, Livestock Fisheries and Forestry, University of the Philippines Los Baños, 4031, Laguna, Philippines
| | - Lavernee S Gueco
- Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, 4031, Laguna, Philippines
| | - Fe M Dela Cueva
- Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, 4031, Laguna, Philippines
| | - Darlon V Lantican
- Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, 4031, Laguna, Philippines
| |
Collapse
|
6
|
Martin G, Cottin A, Baurens FC, Labadie K, Hervouet C, Salmon F, Paulo-de-la-Reberdiere N, Van den Houwe I, Sardos J, Aury JM, D'Hont A, Yahiaoui N. Interspecific introgression patterns reveal the origins of worldwide cultivated bananas in New Guinea. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:802-818. [PMID: 36575919 DOI: 10.1111/tpj.16086] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 12/16/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
Hybridizations between Musa species and subspecies, enabled by their transport via human migration, were proposed to have played an important role in banana domestication. We exploited sequencing data of 226 Musaceae accessions, including wild and cultivated accessions, to characterize the inter(sub)specific hybridization pattern that gave rise to cultivated bananas. We identified 11 genetic pools that contributed to cultivars, including two contributors of unknown origin. Informative alleles for each of these genetic pools were pinpointed and used to obtain genome ancestry mosaics of accessions. Diploid and triploid cultivars had genome mosaics involving three up to possibly seven contributors. The simplest mosaics were found for some diploid cultivars from New Guinea, combining three contributors, i.e., banksii and zebrina representing Musa acuminata subspecies and, more unexpectedly, the New Guinean species Musa schizocarpa. Breakpoints of M. schizocarpa introgressions were found to be conserved between New Guinea cultivars and the other analyzed diploid and triploid cultivars. This suggests that plants bearing these M. schizocarpa introgressions were transported from New Guinea and gave rise to currently cultivated bananas. Many cultivars showed contrasted mosaics with predominant ancestry from their geographical origin across Southeast Asia to New Guinea. This revealed that further diversification occurred in different Southeast Asian regions through hybridization with other Musa (sub)species, including two unknown ancestors that we propose to be M. acuminata ssp. halabanensis and a yet to be characterized M. acuminata subspecies. These results highlighted a dynamic crop formation process that was initiated in New Guinea, with subsequent diversification throughout Southeast Asia.
Collapse
Affiliation(s)
- Guillaume Martin
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Aurélien Cottin
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Franc-Christophe Baurens
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Karine Labadie
- Genoscope, Institut François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Catherine Hervouet
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Frédéric Salmon
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- CIRAD, UMR AGAP Institut, F-97130 Capesterre-Belle-Eau, Guadeloupe, France
| | - Nilda Paulo-de-la-Reberdiere
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- CIRAD, UMR AGAP Institut, CRB-PT, F-97170 Roujol Petit-Bourg, Guadeloupe, France
| | - Ines Van den Houwe
- Bioversity International, Willem De Croylaan 42, B-3001, Leuven, Belgium
| | - Julie Sardos
- Bioversity International, Parc Scientifique Agropolis II, 34397, Montpellier, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Angélique D'Hont
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Nabila Yahiaoui
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| |
Collapse
|
7
|
Colonges K, Seguine E, Saltos A, Davrieux F, Minier J, Jimenez JC, Lahon MC, Calderon D, Subia C, Sotomayor I, Fernández F, Fouet O, Rhoné B, Argout X, Lebrun M, Costet P, Lanaud C, Boulanger R, Loor Solorzano RG. Diversity and determinants of bitterness, astringency, and fat content in cultivated Nacional and native Amazonian cocoa accessions from Ecuador. THE PLANT GENOME 2022; 15:e20218. [PMID: 36065790 DOI: 10.1002/tpg2.20218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 03/28/2022] [Indexed: 06/15/2023]
Abstract
Cocoa (Theobroma cacao L.) is the only tree that can produce cocoa. Cocoa beans are highly sought after by chocolate makers to produce chocolate. Cocoa can be fine aromatic, characterized by floral and fruity notes, or it can be described as standard cocoa with a more pronounced cocoa aroma and bitterness. In this study, the genetic and biochemical determinants of sensorial notes and nonvolatile compounds related to bitterness, astringency, fat content, and protein content will be investigated in two populations: a cultivated modern Nacional population and a population of cocoa accessions collected recently in the Ecuadorian South Amazonia area of origin of the Nacional ancestral variety. For this purpose, a genome-wide association study (GWAS) was carried out on both populations, with results of biochemical compounds evaluated by near-infrared spectroscopy (NIRS) assays and with sensory evaluations. Twenty areas of associations were detected for sensorial data especially bitterness and astringency. Fifty-three areas of associations were detected linked to nonvolatile compounds. A total of 81 candidate genes could be identified in the areas of the association.
Collapse
Affiliation(s)
- Kelly Colonges
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- AGAP Institut, Univ. Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- CIRAD, UMR Qualisud, Montpellier, F-34398, France
- Qualisud, Univ. Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France
| | - Edward Seguine
- Seguine Cacao/Guittard Chocolate Co, Arroyo Grande, CA, USA
| | - Alejandra Saltos
- Instituto Nacional de Investigacion Agropecurias, INIAP, Quito, Ecuador
| | - Fabrice Davrieux
- Qualisud, Univ. Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France
- Cirad, UMR Qualisud, Réunion, F-97400, France
| | - Jérôme Minier
- Qualisud, Univ. Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France
- Cirad, UMR Qualisud, Réunion, F-97400, France
| | | | - Marie-Christine Lahon
- CIRAD, UMR Qualisud, Montpellier, F-34398, France
- Qualisud, Univ. Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France
| | - Darío Calderon
- Instituto Nacional de Investigacion Agropecurias, INIAP, Quito, Ecuador
| | - Cristian Subia
- Instituto Nacional de Investigacion Agropecurias, INIAP, Quito, Ecuador
| | - Ignacio Sotomayor
- Instituto Nacional de Investigacion Agropecurias, INIAP, Quito, Ecuador
| | - Fabián Fernández
- Instituto Nacional de Investigacion Agropecurias, INIAP, Quito, Ecuador
| | - Olivier Fouet
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- AGAP Institut, Univ. Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Bénédicte Rhoné
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- AGAP Institut, Univ. Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Xavier Argout
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- AGAP Institut, Univ. Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Marc Lebrun
- CIRAD, UMR Qualisud, Montpellier, F-34398, France
- Qualisud, Univ. Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France
| | | | - Claire Lanaud
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- AGAP Institut, Univ. Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Renaud Boulanger
- CIRAD, UMR Qualisud, Montpellier, F-34398, France
- Qualisud, Univ. Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France
| | | |
Collapse
|
8
|
Mbo Nkoulou LF, Ngalle HB, Cros D, Adje COA, Fassinou NVH, Bell J, Achigan-Dako EG. Perspective for genomic-enabled prediction against black sigatoka disease and drought stress in polyploid species. FRONTIERS IN PLANT SCIENCE 2022; 13:953133. [PMID: 36388523 PMCID: PMC9650417 DOI: 10.3389/fpls.2022.953133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
Genomic selection (GS) in plant breeding is explored as a promising tool to solve the problems related to the biotic and abiotic threats. Polyploid plants like bananas (Musa spp.) face the problem of drought and black sigatoka disease (BSD) that restrict their production. The conventional plant breeding is experiencing difficulties, particularly phenotyping costs and long generation interval. To overcome these difficulties, GS in plant breeding is explored as an alternative with a great potential for reducing costs and time in selection process. So far, GS does not have the same success in polyploid plants as with diploid plants because of the complexity of their genome. In this review, we present the main constraints to the application of GS in polyploid plants and the prospects for overcoming these constraints. Particular emphasis is placed on breeding for BSD and drought-two major threats to banana production-used in this review as a model of polyploid plant. It emerges that the difficulty in obtaining markers of good quality in polyploids is the first challenge of GS on polyploid plants, because the main tools used were developed for diploid species. In addition to that, there is a big challenge of mastering genetic interactions such as dominance and epistasis effects as well as the genotype by environment interaction, which are very common in polyploid plants. To get around these challenges, we have presented bioinformatics tools, as well as artificial intelligence approaches, including machine learning. Furthermore, a scheme for applying GS to banana for BSD and drought has been proposed. This review is of paramount impact for breeding programs that seek to reduce the selection cycle of polyploids despite the complexity of their genome.
Collapse
Affiliation(s)
- Luther Fort Mbo Nkoulou
- Genetics, Biotechnology, and Seed Science Unit (GBioS), Department of Plant Sciences, Faculty of Agronomic Sciences, University of Abomey Calavi, Cotonou, Benin
- Unit of Genetics and Plant Breeding (UGAP), Department of Plant Biology, Faculty of Sciences, University of Yaoundé 1, Yaoundé, Cameroon
- Institute of Agricultural Research for Development, Centre de Recherche Agricole de Mbalmayo (CRAM), Mbalmayo, Cameroon
| | - Hermine Bille Ngalle
- Unit of Genetics and Plant Breeding (UGAP), Department of Plant Biology, Faculty of Sciences, University of Yaoundé 1, Yaoundé, Cameroon
| | - David Cros
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Unité Mixte de Recherche (UMR) Amélioration Génétique et Adaptation des Plantes méditerranéennes et tropicales (AGAP) Institut, Montpellier, France
- Unité Mixte de Recherche (UMR) Amélioration Génétique et Adaptation des Plantes méditerranéennes et tropicales (AGAP) Institut, University of Montpellier, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut Agro, Montpellier, France
| | - Charlotte O. A. Adje
- Genetics, Biotechnology, and Seed Science Unit (GBioS), Department of Plant Sciences, Faculty of Agronomic Sciences, University of Abomey Calavi, Cotonou, Benin
| | - Nicodeme V. H. Fassinou
- Genetics, Biotechnology, and Seed Science Unit (GBioS), Department of Plant Sciences, Faculty of Agronomic Sciences, University of Abomey Calavi, Cotonou, Benin
| | - Joseph Bell
- Unit of Genetics and Plant Breeding (UGAP), Department of Plant Biology, Faculty of Sciences, University of Yaoundé 1, Yaoundé, Cameroon
| | - Enoch G. Achigan-Dako
- Genetics, Biotechnology, and Seed Science Unit (GBioS), Department of Plant Sciences, Faculty of Agronomic Sciences, University of Abomey Calavi, Cotonou, Benin
| |
Collapse
|
9
|
A Flashforward Look into Solutions for Fruit and Vegetable Production. Genes (Basel) 2022; 13:genes13101886. [PMID: 36292770 PMCID: PMC9602186 DOI: 10.3390/genes13101886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/26/2022] [Accepted: 10/13/2022] [Indexed: 12/02/2022] Open
Abstract
One of the most important challenges facing current and future generations is how climate change and continuous population growth adversely affect food security. To address this, the food system needs a complete transformation where more is produced in non-optimal and space-limited areas while reducing negative environmental impacts. Fruits and vegetables, essential for human health, are high-value-added crops, which are grown in both greenhouses and open field environments. Here, we review potential practices to reduce the impact of climate variation and ecosystem damages on fruit and vegetable crop yield, as well as highlight current bottlenecks for indoor and outdoor agrosystems. To obtain sustainability, high-tech greenhouses are increasingly important and biotechnological means are becoming instrumental in designing the crops of tomorrow. We discuss key traits that need to be studied to improve agrosystem sustainability and fruit yield.
Collapse
|
10
|
Droc G, Martin G, Guignon V, Summo M, Sempéré G, Durant E, Soriano A, Baurens FC, Cenci A, Breton C, Shah T, Aury JM, Ge XJ, Harrison PH, Yahiaoui N, D’Hont A, Rouard M. The banana genome hub: a community database for genomics in the Musaceae. HORTICULTURE RESEARCH 2022; 9:uhac221. [PMID: 36479579 PMCID: PMC9720444 DOI: 10.1093/hr/uhac221] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 09/22/2022] [Indexed: 06/17/2023]
Abstract
The Banana Genome Hub provides centralized access for genome assemblies, annotations, and the extensive related omics resources available for bananas and banana relatives. A series of tools and unique interfaces are implemented to harness the potential of genomics in bananas, leveraging the power of comparative analysis, while recognizing the differences between datasets. Besides effective genomic tools like BLAST and the JBrowse genome browser, additional interfaces enable advanced gene search and gene family analyses including multiple alignments and phylogenies. A synteny viewer enables the comparison of genome structures between chromosome-scale assemblies. Interfaces for differential expression analyses, metabolic pathways and GO enrichment were also added. A catalogue of variants spanning the banana diversity is made available for exploration, filtering, and export to a wide variety of software. Furthermore, we implemented new ways to graphically explore gene presence-absence in pangenomes as well as genome ancestry mosaics for cultivated bananas. Besides, to guide the community in future sequencing efforts, we provide recommendations for nomenclature of locus tags and a curated list of public genomic resources (assemblies, resequencing, high density genotyping) and upcoming resources-planned, ongoing or not yet public. The Banana Genome Hub aims at supporting the banana scientific community for basic, translational, and applied research and can be accessed at https://banana-genome-hub.southgreen.fr.
Collapse
Affiliation(s)
| | - Guillaume Martin
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
| | - Valentin Guignon
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier, France
| | - Marilyne Summo
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
| | - Guilhem Sempéré
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
- CIRAD, UMR INTERTRYP, F-34398 Montpellier, France
- INTERTRYP, Université de Montpellier, CIRAD, IRD, 34398 Montpellier, France
| | - Eloi Durant
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
- Syngenta Seeds SAS, Saint-Sauveur, 31790, France
- DIADE, Univ Montpellier, CIRAD, IRD, Montpellier, 34830, France
| | - Alexandre Soriano
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
| | - Franc-Christophe Baurens
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
| | - Alberto Cenci
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier, France
| | - Catherine Breton
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier, France
| | | | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510520, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510520, China
| | - Pat Heslop Harrison
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510520, China
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Nabila Yahiaoui
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
| | - Angélique D’Hont
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
| | | |
Collapse
|
11
|
Hou BH, Tsai YH, Chiang MH, Tsao SM, Huang SH, Chao CP, Chen HM. Cultivar-specific markers, mutations, and chimerisim of Cavendish banana somaclonal variants resistant to Fusarium oxysporum f. sp. cubense tropical race 4. BMC Genomics 2022; 23:470. [PMID: 35752751 PMCID: PMC9233791 DOI: 10.1186/s12864-022-08692-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 06/13/2022] [Indexed: 11/13/2022] Open
Abstract
Background The selection of tissue culture–derived somaclonal variants of Giant Cavendish banana (Musa spp., Cavendish sub-group AAA) by the Taiwan Banana Research Institute (TBRI) has resulted in several cultivars resistant to Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4), a destructive fungus threatening global banana production. However, the mutations in these somaclonal variants have not yet been determined. We performed an RNA-sequencing (RNA-seq) analysis of three TBRI Foc TR4–resistant cultivars: ‘Tai-Chiao No. 5’ (TC5), ‘Tai-Chiao No. 7’ (TC7), and ‘Formosana’ (FM), as well as their susceptible progenitor ‘Pei-Chiao’ (PC), to investigate the sequence variations among them and develop cultivar-specific markers. Results A group of single-nucleotide variants (SNVs) specific to one cultivar were identified from the analysis of RNA-seq data and validated using Sanger sequencing from genomic DNA. Several SNVs were further converted into cleaved amplified polymorphic sequence (CAPS) markers or derived CAPS markers that could identify the three Foc TR4–resistant cultivars among 6 local and 5 international Cavendish cultivars. Compared with PC, the three resistant cultivars showed a loss or alteration of heterozygosity in some chromosomal regions, which appears to be a consequence of single-copy chromosomal deletions. Notably, TC7 and FM shared a common deletion region on chromosome 5; however, different TC7 tissues displayed varying degrees of allele ratios in this region, suggesting the presence of chimerism in TC7. Conclusions This work demonstrates that reliable SNV markers of tissue culture–derived and propagated banana cultivars with a triploid genome can be developed through RNA-seq data analysis. Moreover, the analysis of sequence heterozygosity can uncover chromosomal deletions and chimerism in banana somaclonal variants. The markers obtained from this study will assist with the identification of TBRI Cavendish somaclonal variants for the quality control of tissue culture propagation, and the protection of breeders’ rights. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08692-5.
Collapse
Affiliation(s)
- Bo-Han Hou
- Agricultural Biotechnology Research Center, Academia Sinica, 11529, Taipei, Taiwan
| | - Yi-Heng Tsai
- Agricultural Biotechnology Research Center, Academia Sinica, 11529, Taipei, Taiwan
| | - Ming-Hau Chiang
- Agricultural Biotechnology Research Center, Academia Sinica, 11529, Taipei, Taiwan
| | - Shu-Ming Tsao
- Agricultural Biotechnology Research Center, Academia Sinica, 11529, Taipei, Taiwan
| | | | - Chih-Ping Chao
- Taiwan Banana Research Institute, 90442, Pingtung, Taiwan
| | - Ho-Ming Chen
- Agricultural Biotechnology Research Center, Academia Sinica, 11529, Taipei, Taiwan.
| |
Collapse
|
12
|
Morphoanatomy and Histochemistry of Septal Nectaries Related to Female Fertility in Banana Plants of the ‘Cavendish’ Subgroup. PLANTS 2022; 11:plants11091177. [PMID: 35567177 PMCID: PMC9104050 DOI: 10.3390/plants11091177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/07/2022] [Accepted: 04/20/2022] [Indexed: 11/16/2022]
Abstract
The objective of this study was to gain a deeper understanding of the morphoanatomical and histochemical structures that compose the nectary of pistillate flowers (female), which are involved in the female fertility of banana plants belonging to the ‘Cavendish’ subgroup. The diploid Calcutta 4 and the Grand Naine cultivar were used for the assessment. Five stages of floral development were proposed. Pistillate flower nectaries were subjected to morphological characterization, morphoanatomy, and histochemical tests (phenolic compounds, proteins, and lipids). Morphoanatomical analysis revealed a greater presence of narrow nectariferous ducts and more developed pluristratified papillae in Calcutta 4. In contrast, Grand Naine displayed cell disintegration in nectariferous ducts and pluristratified papillae, absent transmitting tissue, and greater amounts of vascular bundles at anthesis. However, Calcutta 4 displayed no changes in the nectariferous duct at any of the stages. An association was found between phenolic compounds and lipids in vacuoles adjacent to the vascular bundles, with greater amounts found in Grand Naine. The localization of phenolic compounds may suggest that these compounds play a role in nectar secretion or the oxidation of the nectary region, ultimately limiting the growth and passage of the pollen tube and preventing ovule fertilization.
Collapse
|
13
|
Sempéré G, Larmande P, Rouard M. Managing High-Density Genotyping Data with Gigwa. Methods Mol Biol 2022; 2443:415-427. [PMID: 35037218 DOI: 10.1007/978-1-0716-2067-0_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Next generation sequencing technologies enabled high-density genotyping for large numbers of samples. Nowadays SNP calling pipelines produce up to millions of such markers, but which need to be filtered in various ways according to the type of analyses. One of the main challenges still lies in the management of an increasing volume of genotyping files that are difficult to handle for many applications. Here, we provide a practical guide for efficiently managing large genomic variation data using Gigwa, a user-friendly, scalable and versatile application that may be deployed either remotely on web servers or on a local machine.
Collapse
Affiliation(s)
- Guilhem Sempéré
- CIRAD, UMR INTERTRYP, Montpellier, France
- INTERTRYP, Univ Montpellier, CIRAD, IRD, Montpellier, France
- French Institute of Bioinformatics (IFB)-South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, Montpellier, France
| | - Pierre Larmande
- French Institute of Bioinformatics (IFB)-South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, Montpellier, France.
- DIADE, Univ Montpellier, IRD, Montpellier, France.
| | - Mathieu Rouard
- French Institute of Bioinformatics (IFB)-South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, Montpellier, France
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, France
| |
Collapse
|
14
|
Uwimana B, Mwanje G, Batte M, Akech V, Shah T, Vuylsteke M, Swennen R. Continuous Mapping Identifies Loci Associated With Weevil Resistance [ Cosmopolites sordidus (Germar)] in a Triploid Banana Population. FRONTIERS IN PLANT SCIENCE 2021; 12:753241. [PMID: 34912355 PMCID: PMC8667469 DOI: 10.3389/fpls.2021.753241] [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: 08/04/2021] [Accepted: 10/14/2021] [Indexed: 06/14/2023]
Abstract
The first step toward marker-assisted selection is linking the phenotypes to molecular markers through quantitative trait loci (QTL) analysis. While the process is straightforward in self-pollinating diploid (2x) species, QTL analysis in polyploids requires unconventional methods. In this study, we have identified markers associated with weevil Cosmopolites sordidus (Germar) resistance in bananas using 138 triploid (2n = 3x) hybrids derived from a cross between a tetraploid "Monyet" (2n = 4x) and a 2x "Kokopo" (2n = 2x) banana genotypes. The population was genotyped by Diversity Arrays Technology Sequencing (DArTSeq), resulting in 18,009 polymorphic single nucleotide polymorphisms (SNPs) between the two parents. Marker-trait association was carried out by continuous mapping where the adjusted trait means for the corm peripheral damage (PD) and total cross-section damage (TXD), both on the logit scale, were regressed on the marker allele frequencies. Forty-four SNPs that were associated with corm PD were identified on the chromosomes 5, 6, and 8, with 41 of them located on chromosome 6 and segregated in "Kokopo." Eleven SNPs associated with corm total TXD were identified on chromosome 6 and segregated in "Monyet." The additive effect of replacing one reference allele with the alternative allele was determined at each marker position. The PD QTL was confirmed using conventional QTL linkage analysis in the simplex markers segregating in "Kokopo" (AAAA × RA). We also identified 43 putative genes in the vicinity of the markers significantly associated with the two traits. The identified loci associated with resistance to weevil damage will be used in the efforts of developing molecular tools for marker-assisted breeding in bananas.
Collapse
Affiliation(s)
- Brigitte Uwimana
- International Institute of Tropical Agriculture (IITA), Kampala, Uganda
| | - Gerald Mwanje
- International Institute of Tropical Agriculture (IITA), Kampala, Uganda
| | - Michael Batte
- International Institute of Tropical Agriculture (IITA), Kampala, Uganda
| | - Violet Akech
- International Institute of Tropical Agriculture (IITA), Kampala, Uganda
| | - Trushar Shah
- International Institute of Tropical Agriculture (IITA), International Livestock Research Institute Campus, Nairobi, Kenya
| | | | - Rony Swennen
- International Institute of Tropical Agriculture (IITA), Kampala, Uganda
- Department of Crop Biosystems, KU Leuven, Heverlee, Belgium
| |
Collapse
|
15
|
Mondo JM, Agre PA, Asiedu R, Akoroda MO, Asfaw A. Genome-Wide Association Studies for Sex Determination and Cross-Compatibility in Water Yam ( Dioscorea alata L.). PLANTS (BASEL, SWITZERLAND) 2021; 10:1412. [PMID: 34371615 PMCID: PMC8309230 DOI: 10.3390/plants10071412] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/06/2021] [Accepted: 07/08/2021] [Indexed: 11/17/2022]
Abstract
Yam (Dioscorea spp.) species are predominantly dioecious, with male and female flowers borne on separate individuals. Cross-pollination is, therefore, essential for gene flow among and within yam species to achieve breeding objectives. Understanding genetic mechanisms underlying sex determination and cross-compatibility is crucial for planning a successful hybridization program. This study used the genome-wide association study (GWAS) approach for identifying genomic regions linked to sex and cross-compatibility in water yam (Dioscorea alata L.). We identified 54 markers linked to flower sex determination, among which 53 markers were on chromosome 6 and one on chromosome 11. Our result ascertained that D. alata is characterized by the male heterogametic sex determination system (XX/XY). The cross-compatibility indices, average crossability rate (ACR) and percentage high crossability (PHC), were controlled by loci on chromosomes 1, 6 and 17. Of the significant loci, SNPs located on chromosomes 1 and 17 were the most promising for ACR and PHC, respectively, and should be validated for use in D. alata hybridization activities to predict cross-compatibility success. A total of 61 putative gene/protein families with direct or indirect influence on plant reproduction were annotated in chromosomic regions controlling the target traits. This study provides valuable insights into the genetic control of D. alata sexual reproduction. It opens an avenue for developing genomic tools for predicting hybridization success in water yam breeding programs.
Collapse
Affiliation(s)
- Jean M. Mondo
- International Institute of Tropical Agriculture (IITA), Ibadan 5320, Nigeria; (J.M.M.); (R.A.); (A.A.)
- Institute of Life and Earth Sciences, Pan African University, University of Ibadan, Ibadan 200284, Nigeria
- Department of Crop Production, Université Evangélique en Afrique (UEA), Bukavu 3323, Democratic Republic of the Congo
| | - Paterne A. Agre
- International Institute of Tropical Agriculture (IITA), Ibadan 5320, Nigeria; (J.M.M.); (R.A.); (A.A.)
| | - Robert Asiedu
- International Institute of Tropical Agriculture (IITA), Ibadan 5320, Nigeria; (J.M.M.); (R.A.); (A.A.)
| | | | - Asrat Asfaw
- International Institute of Tropical Agriculture (IITA), Ibadan 5320, Nigeria; (J.M.M.); (R.A.); (A.A.)
| |
Collapse
|
16
|
Ogbonna AC, Braatz de Andrade LR, Mueller LA, de Oliveira EJ, Bauchet GJ. Comprehensive genotyping of a Brazilian cassava (Manihot esculenta Crantz) germplasm bank: insights into diversification and domestication. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1343-1362. [PMID: 33575821 PMCID: PMC8081687 DOI: 10.1007/s00122-021-03775-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 01/11/2021] [Indexed: 05/03/2023]
Abstract
KEY MESSAGE Brazilian cassava diversity was characterized through population genetics and clustering approaches, highlighting contrasted genetic groups and spatial genetic differentiation. Cassava (Manihot esculenta Crantz) is a major staple root crop of the tropics, originating from the Amazonian region. In this study, 3354 cassava landraces and modern breeding lines from the Embrapa Cassava Germplasm Bank (CGB) were characterized. All individuals were subjected to genotyping-by-sequencing (GBS), identifying 27,045 single-nucleotide polymorphisms (SNPs). Identity-by-state and population structure analyses revealed a unique set of 1536 individuals and 10 distinct genetic groups with heterogeneous linkage disequilibrium (LD). On this basis, a density of 1300-4700 SNP markers were selected for large-effect quantitative trait loci (QTL) detection. Identified genetic groups were further characterized for population genetics parameters including minor allele frequency (MAF), observed heterozygosity [Formula: see text], effective population size estimate [Formula: see text]) and polymorphism information content (PIC). Selection footprints and introgressions of M. glaziovii were detected. Spatial population structure analysis revealed five ancestral populations related to distinct Brazilian ecoregions. Estimation of historical relationships among identified populations suggests an early population split from Amazonian to Atlantic forest and Caatinga ecoregions and active gene flows. This study provides a thorough genetic characterization of ex situ germplasm resources from cassava's center of origin, South America, with results shedding light on Brazilian cassava characteristics and its biogeographical landscape. These findings support and facilitate the use of genetic resources in modern breeding programs including implementation of association mapping and genomic selection strategies.
Collapse
Affiliation(s)
- Alex C Ogbonna
- Cornell University, Ithaca, NY, USA
- Boyce Thompson Institute for Plant Research, Ithaca, NY, USA
| | | | - Lukas A Mueller
- Cornell University, Ithaca, NY, USA
- Boyce Thompson Institute for Plant Research, Ithaca, NY, USA
| | | | | |
Collapse
|
17
|
Ogbonna AC, Braatz de Andrade LR, Mueller LA, de Oliveira EJ, Bauchet GJ. Comprehensive genotyping of a Brazilian cassava (Manihot esculenta Crantz) germplasm bank: insights into diversification and domestication. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1343-1362. [PMID: 33575821 DOI: 10.1101/2020.07.13.200816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 01/11/2021] [Indexed: 05/25/2023]
Abstract
Brazilian cassava diversity was characterized through population genetics and clustering approaches, highlighting contrasted genetic groups and spatial genetic differentiation. Cassava (Manihot esculenta Crantz) is a major staple root crop of the tropics, originating from the Amazonian region. In this study, 3354 cassava landraces and modern breeding lines from the Embrapa Cassava Germplasm Bank (CGB) were characterized. All individuals were subjected to genotyping-by-sequencing (GBS), identifying 27,045 single-nucleotide polymorphisms (SNPs). Identity-by-state and population structure analyses revealed a unique set of 1536 individuals and 10 distinct genetic groups with heterogeneous linkage disequilibrium (LD). On this basis, a density of 1300-4700 SNP markers were selected for large-effect quantitative trait loci (QTL) detection. Identified genetic groups were further characterized for population genetics parameters including minor allele frequency (MAF), observed heterozygosity [Formula: see text], effective population size estimate [Formula: see text]) and polymorphism information content (PIC). Selection footprints and introgressions of M. glaziovii were detected. Spatial population structure analysis revealed five ancestral populations related to distinct Brazilian ecoregions. Estimation of historical relationships among identified populations suggests an early population split from Amazonian to Atlantic forest and Caatinga ecoregions and active gene flows. This study provides a thorough genetic characterization of ex situ germplasm resources from cassava's center of origin, South America, with results shedding light on Brazilian cassava characteristics and its biogeographical landscape. These findings support and facilitate the use of genetic resources in modern breeding programs including implementation of association mapping and genomic selection strategies.
Collapse
Affiliation(s)
- Alex C Ogbonna
- Cornell University, Ithaca, NY, USA
- Boyce Thompson Institute for Plant Research, Ithaca, NY, USA
| | | | - Lukas A Mueller
- Cornell University, Ithaca, NY, USA
- Boyce Thompson Institute for Plant Research, Ithaca, NY, USA
| | | | | |
Collapse
|
18
|
Recent Large-Scale Genotyping and Phenotyping of Plant Genetic Resources of Vegetatively Propagated Crops. PLANTS 2021; 10:plants10020415. [PMID: 33672381 PMCID: PMC7926561 DOI: 10.3390/plants10020415] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/19/2021] [Accepted: 02/19/2021] [Indexed: 12/12/2022]
Abstract
Several recent national and international projects have focused on large-scale genotyping of plant genetic resources in vegetatively propagated crops like fruit and berries, potatoes and woody ornamentals. The primary goal is usually to identify true-to-type plant material, detect possible synonyms, and investigate genetic diversity and relatedness among accessions. A secondary goal may be to create sustainable databases that can be utilized in research and breeding for several years ahead. Commonly applied DNA markers (like microsatellite DNA and SNPs) and next-generation sequencing each have their pros and cons for these purposes. Methods for large-scale phenotyping have lagged behind, which is unfortunate since many commercially important traits (yield, growth habit, storability, and disease resistance) are difficult to score. Nevertheless, the analysis of gene action and development of robust DNA markers depends on environmentally controlled screening of very large sets of plant material. Although more time-consuming, co-operative projects with broad-scale data collection are likely to produce more reliable results. In this review, we will describe some of the approaches taken in genotyping and/or phenotyping projects concerning a wide variety of vegetatively propagated crops.
Collapse
|
19
|
Martin G, Baurens F, Hervouet C, Salmon F, Delos J, Labadie K, Perdereau A, Mournet P, Blois L, Dupouy M, Carreel F, Ricci S, Lemainque A, Yahiaoui N, D’Hont A. Chromosome reciprocal translocations have accompanied subspecies evolution in bananas. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:1698-1711. [PMID: 33067829 PMCID: PMC7839431 DOI: 10.1111/tpj.15031] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 10/02/2020] [Indexed: 05/09/2023]
Abstract
Chromosome rearrangements and the way that they impact genetic differentiation and speciation have long raised questions from evolutionary biologists. They are also a major concern for breeders because of their bearing on chromosome recombination. Banana is a major crop that derives from inter(sub)specific hybridizations between various once geographically isolated Musa species and subspecies. We sequenced 155 accessions, including banana cultivars and representatives of Musa diversity, and genotyped-by-sequencing 1059 individuals from 11 progenies. We precisely characterized six large reciprocal translocations and showed that they emerged in different (sub)species of Musa acuminata, the main contributor to currently cultivated bananas. Most diploid and triploid cultivars analyzed were structurally heterozygous for 1 to 4 M. acuminata translocations, highlighting their complex origin. We showed that all translocations induced a recombination reduction of variable intensity and extent depending on the translocations, involving only the breakpoint regions, a chromosome arm, or an entire chromosome. The translocated chromosomes were found preferentially transmitted in many cases. We explore and discuss the possible mechanisms involved in this preferential transmission and its impact on translocation colonization.
Collapse
Affiliation(s)
- Guillaume Martin
- CIRADUMR AGAPMontpellierF‐34398France
- AGAPUniv MontpellierCIRADINRAEInstitut AgroMontpellier34060France
| | - Franc‐Christophe Baurens
- CIRADUMR AGAPMontpellierF‐34398France
- AGAPUniv MontpellierCIRADINRAEInstitut AgroMontpellier34060France
| | - Catherine Hervouet
- CIRADUMR AGAPMontpellierF‐34398France
- AGAPUniv MontpellierCIRADINRAEInstitut AgroMontpellier34060France
| | - Frédéric Salmon
- AGAPUniv MontpellierCIRADINRAEInstitut AgroMontpellier34060France
- CIRADUMR AGAPCapesterre‐Belle‐EauGuadeloupeF‐97130France
| | - Jean‐Marie Delos
- AGAPUniv MontpellierCIRADINRAEInstitut AgroMontpellier34060France
- CIRADUMR AGAPCapesterre‐Belle‐EauGuadeloupeF‐97130France
| | - Karine Labadie
- GenoscopeInstitut de biologie François JacobCommissariat à l'Energie Atomique (CEA)Université Paris‐SaclayEvryFrance
| | - Aude Perdereau
- GenoscopeInstitut de biologie François JacobCommissariat à l'Energie Atomique (CEA)Université Paris‐SaclayEvryFrance
| | - Pierre Mournet
- CIRADUMR AGAPMontpellierF‐34398France
- AGAPUniv MontpellierCIRADINRAEInstitut AgroMontpellier34060France
| | - Louis Blois
- CIRADUMR AGAPMontpellierF‐34398France
- AGAPUniv MontpellierCIRADINRAEInstitut AgroMontpellier34060France
| | - Marion Dupouy
- CIRADUMR AGAPMontpellierF‐34398France
- AGAPUniv MontpellierCIRADINRAEInstitut AgroMontpellier34060France
| | - Françoise Carreel
- CIRADUMR AGAPMontpellierF‐34398France
- AGAPUniv MontpellierCIRADINRAEInstitut AgroMontpellier34060France
| | - Sébastien Ricci
- AGAPUniv MontpellierCIRADINRAEInstitut AgroMontpellier34060France
- CIRADUMR AGAPCapesterre‐Belle‐EauGuadeloupeF‐97130France
| | - Arnaud Lemainque
- GenoscopeInstitut de biologie François JacobCommissariat à l'Energie Atomique (CEA)Université Paris‐SaclayEvryFrance
| | - Nabila Yahiaoui
- CIRADUMR AGAPMontpellierF‐34398France
- AGAPUniv MontpellierCIRADINRAEInstitut AgroMontpellier34060France
| | - Angélique D’Hont
- CIRADUMR AGAPMontpellierF‐34398France
- AGAPUniv MontpellierCIRADINRAEInstitut AgroMontpellier34060France
| |
Collapse
|
20
|
Hou L, Chen W, Zhang Z, Pang X, Li Y. Genome-wide association studies of fruit quality traits in jujube germplasm collections using genotyping-by-sequencing. THE PLANT GENOME 2020; 13:e20036. [PMID: 33217218 DOI: 10.1002/tpg2.20036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 05/06/2020] [Accepted: 05/24/2020] [Indexed: 06/11/2023]
Abstract
Chinese jujube (Ziziphus jujuba Mill.) is an important fruit crop and harbors many highly diverse traits of potential economic importance. Fruit size, stone size, and fruit cracking have an important influence on the commercial value of jujube. This study is the first to conduct a genome-wide association study (GWAS) on 180 accessions of jujube and focuses on locating single-nucleotide polymorphisms (SNPs) associated with nine important fruit quality traits. Genotyping was performed using genotyping-by-sequencing and 4651 high-quality SNPs were identified. A genetic diversity analysis revealed the presence of three distinct groups, and rapid linkage disequilibrium decay was observed in this jujube population. Using a mixed linear model, a total of 45 significant SNP-trait associations were detected, among which 33 SNPs had associations with fruit size-related traits, nine were associated with stone size-related traits, and three with fruit cracking-related traits. In total, 21 candidate genes involved in cell expansion, abiotic stress responses, hormone signaling, and growth development were identified from the genome sequences of jujube. These results are useful as basic data for GWAS of other jujube traits, and these significant SNP loci and candidate genes should aid marker-assisted breeding and genomic selection of improved jujube cultivars.
Collapse
Affiliation(s)
- Lu Hou
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Wu Chen
- The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Zhiyong Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Xiaoming Pang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yingyue Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| |
Collapse
|
21
|
Sempéré G, Pétel A, Rouard M, Frouin J, Hueber Y, De Bellis F, Larmande P. Gigwa v2-Extended and improved genotype investigator. Gigascience 2019; 8:5488103. [PMID: 31077313 PMCID: PMC6511067 DOI: 10.1093/gigascience/giz051] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/19/2019] [Accepted: 04/08/2019] [Indexed: 11/19/2022] Open
Abstract
Background The study of genetic variations is the basis of many research domains in biology. From genome structure to population dynamics, many applications involve the use of genetic variants. The advent of next-generation sequencing technologies led to such a flood of data that the daily work of scientists is often more focused on data management than data analysis. This mass of genotyping data poses several computational challenges in terms of storage, search, sharing, analysis, and visualization. While existing tools try to solve these challenges, few of them offer a comprehensive and scalable solution. Results Gigwa v2 is an easy-to-use, species-agnostic web application for managing and exploring high-density genotyping data. It can handle multiple databases and may be installed on a local computer or deployed as an online data portal. It supports various standard import and export formats, provides advanced filtering options, and offers means to visualize density charts or push selected data into various stand-alone or online tools. It implements 2 standard RESTful application programming interfaces, GA4GH, which is health-oriented, and BrAPI, which is breeding-oriented, thus offering wide possibilities of interaction with third-party applications. The project home page provides a list of live instances allowing users to test the system on public data (or reasonably sized user-provided data). Conclusions This new version of Gigwa provides a more intuitive and more powerful way to explore large amounts of genotyping data by offering a scalable solution to search for genotype patterns, functional annotations, or more complex filtering. Furthermore, its user-friendliness and interoperability make it widely accessible to the life science community.
Collapse
Affiliation(s)
- Guilhem Sempéré
- Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR INTERTRYP, F-34398 Montpellier, France.,South Green Bioinformatics Platform, Bioversity, CIRAD, Institut National de la Recherche Agronomique (INRA), IRD, Montpellier, France.,INTERTRYP, Univ Montpellier, CIRAD, Institut de Recherche pour le Développpement (IRD), Montpellier, France
| | - Adrien Pétel
- South Green Bioinformatics Platform, Bioversity, CIRAD, Institut National de la Recherche Agronomique (INRA), IRD, Montpellier, France.,DIADE, Univ Montpellier, IRD, 911 Avenue Agropolis, 34394 Montpellier, France
| | - Mathieu Rouard
- South Green Bioinformatics Platform, Bioversity, CIRAD, Institut National de la Recherche Agronomique (INRA), IRD, Montpellier, France.,Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - Julien Frouin
- CIRAD, UMR AGAP, F-34398 Montpellier, France.,AGAP, Univ Montpellier, CIRAD, INRA, Institut national d'études supérieures agronomiques de Montpellier (Montpellier SupAgro), Montpellier, France
| | - Yann Hueber
- South Green Bioinformatics Platform, Bioversity, CIRAD, Institut National de la Recherche Agronomique (INRA), IRD, Montpellier, France.,Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - Fabien De Bellis
- CIRAD, UMR AGAP, F-34398 Montpellier, France.,AGAP, Univ Montpellier, CIRAD, INRA, Institut national d'études supérieures agronomiques de Montpellier (Montpellier SupAgro), Montpellier, France
| | - Pierre Larmande
- South Green Bioinformatics Platform, Bioversity, CIRAD, Institut National de la Recherche Agronomique (INRA), IRD, Montpellier, France.,DIADE, Univ Montpellier, IRD, 911 Avenue Agropolis, 34394 Montpellier, France
| |
Collapse
|
22
|
Nyine M, Uwimana B, Akech V, Brown A, Ortiz R, Doležel J, Lorenzen J, Swennen R. Association genetics of bunch weight and its component traits in East African highland banana (Musa spp. AAA group). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:3295-3308. [PMID: 31529270 PMCID: PMC6820618 DOI: 10.1007/s00122-019-03425-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 09/06/2019] [Indexed: 05/06/2023]
Abstract
The major quantitative trait loci associated with bunch weight and its component traits in the East African highland banana-breeding population are located on chromosome 3. Bunch weight increase is one of the major objectives of banana improvement programs, but little is known about the loci controlling bunch weight and its component traits. Here we report for the first time some genomic loci associated with bunch weight and its component traits in banana as revealed through a genome-wide association study. A banana-breeding population of 307 genotypes varying in ploidy was phenotyped in three locations under different environmental conditions, and data were collected on bunch weight, number of hands and fruits; fruit length and circumference; and diameter of both fruit and pulp for three crop cycles. The population was genotyped with genotyping by sequencing and 27,178 single nucleotide polymorphisms (SNPs) were generated. The association between SNPs and the best linear unbiased predictors of traits was performed with TASSEL v5 using a mixed linear model accounting for population structure and kinship. Using Bonferroni correction, false discovery rate, and long-range linkage disequilibrium (LD), 25 genomic loci were identified with significant SNPs and most were localized on chromosome 3. Most SNPs were located in genes encoding uncharacterized and hypothetical proteins, but some mapped to transcription factors and genes involved in cell cycle regulation. Inter-chromosomal LD of SNPs was present in the population, but none of the SNPs were significantly associated with the traits. The clustering of significant SNPs on chromosome 3 supported our hypothesis that fruit filling in this population was under control of a few quantitative trait loci with major effects.
Collapse
Affiliation(s)
- Moses Nyine
- International Institute of Tropical Agriculture, P.O. Box 7878, Kampala, Uganda
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Brigitte Uwimana
- International Institute of Tropical Agriculture, P.O. Box 7878, Kampala, Uganda
| | - Violet Akech
- International Institute of Tropical Agriculture, P.O. Box 7878, Kampala, Uganda
| | - Allan Brown
- International Institute of Tropical Agriculture c/o Nelson Mandela African Institution of Science and Technology, P.O. Box 447, Arusha, Tanzania
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 101, 23053, Alnarp, Sweden
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, 78371, Olomouc, Czech Republic
| | - Jim Lorenzen
- International Institute of Tropical Agriculture, P.O. Box 7878, Kampala, Uganda
- Bill and Melinda Gates Foundation, Seattle, 23350, USA
| | - Rony Swennen
- International Institute of Tropical Agriculture c/o Nelson Mandela African Institution of Science and Technology, P.O. Box 447, Arusha, Tanzania.
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, Katholieke Universiteit, 3001, Leuven, Belgium.
- Bioversity International, 3001, Leuven, Belgium.
| |
Collapse
|
23
|
Aubry S. The Future of Digital Sequence Information for Plant Genetic Resources for Food and Agriculture. FRONTIERS IN PLANT SCIENCE 2019; 10:1046. [PMID: 31543884 PMCID: PMC6728410 DOI: 10.3389/fpls.2019.01046] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 07/29/2019] [Indexed: 05/27/2023]
Abstract
The recent debates on the legal status of "digital sequence information" (DSI) at the international level could have extensive consequences for the future of agriculture and food security. A large majority of recent advances in biology, medicine, or agriculture were achieved by sharing and mining of freely accessible sequencing data. It is most probably because of the tremendous success of modern genomics and advances of synthetic biology that concerns were raised about possible fair and equitable ways of sharing data. The DSI concept is relatively new, and all concerned parties agreed upon the need for a clear definition. For example, the extent to which DSI understanding is limited only to genetic sequence data has to be clarified. In this paper, I focus on a subset of DSI essential to humankind: the DSI originating from plant genetic resources for food and agriculture (PGRFA). Two international agreements shape the conservation and use of plant genetic resources: the Convention on Biodiversity and the International Treaty for Plant Genetic Resources for Food and Agriculture. In an attempt to mobilize DSI users and producers involved in research, breeding, and conservation, I describe here how the increasing amount of genomic data, information, and studies interact with the existing legal framework at the global level. Using possible scenarios, I will emphasize the complexity of the issues surrounding DSI for PGRFA and propose potential ways forward for developing an inclusive governance and fair use of these genetic resources.
Collapse
Affiliation(s)
- Sylvain Aubry
- Department of Plant and Microbial Science, University of Zurich, Zurich, Switzerland
- Section Genetic Resources and Technology, Swiss Federal Office for Agriculture, Bern, Switzerland
| |
Collapse
|
24
|
Wen B, Song W, Sun M, Chen M, Mu Q, Zhang X, Wu Q, Chen X, Gao D, Wu H. Identification and characterization of cherry (Cerasus pseudocerasus G. Don) genes responding to parthenocarpy induced by GA3 through transcriptome analysis. BMC Genet 2019; 20:65. [PMID: 31370778 PMCID: PMC6670208 DOI: 10.1186/s12863-019-0746-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 04/29/2019] [Indexed: 12/02/2022] Open
Abstract
Background Fruit set after successful pollination is key for the production of sweet cherries, and a low fruit-setting rate is the main problem in production of this crop. As gibberellin treatment can directly induce parthenogenesis and satisfy the hormone requirement during fruit growth and development, such treatment is an important strategy for improving the fruit-setting rate of sweet cherries. Previous studies have mainly focused on physiological aspects, such as fruit quality, fruit size, and anatomical structure, whereas the molecular mechanism remains clear. Results In this study, we analyzed the transcriptome of ‘Meizao’ sweet cherry fruit treated with gibberellin during the anthesis and hard-core periods to identify genes associated with parthenocarpic fruit set. A total of 25,341 genes were identified at the anthesis and hard-core stages, 765 (681 upregulated, 84 downregulated) and 186 (141 upregulated, 45 downregulated) of which were significant differentially expressed genes (DEGs) at the anthesis and the hard-core stages after gibberellin 3 (GA3) treatment, respectively. Based on DEGs between the control and GA3 treatments, the GA3 response mainly involves parthenocarpic fruit set and cell division. Exogenous gibberellin stimulated sweet cherry fruit parthenocarpy and enlargement, as verified by qRT-PCR results of related genes as well as the parthenocarpic fruit set and fruit size. Based on our research and previous studies in Arabidopsis thaliana, we identified key genes associated with parthenocarpic fruit set and cell division. Interestingly, we observed patterns among sweet cherry fruit setting-related DEGs, especially those associated with hormone balance, cytoskeleton formation and cell wall modification. Conclusions Overall, the result provides a possible molecular mechanism regulating parthenocarpic fruit set that will be important for basic research and industrial development of sweet cherries. Electronic supplementary material The online version of this article (10.1186/s12863-019-0746-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Binbin Wen
- College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China.,State Key Laboratory of Crop Biology, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China
| | - Wenliang Song
- College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China.,State Key Laboratory of Crop Biology, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China
| | - Mingyue Sun
- College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China.,State Key Laboratory of Crop Biology, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China
| | - Min Chen
- College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China.,State Key Laboratory of Crop Biology, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China
| | - Qin Mu
- College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China
| | - Xinhao Zhang
- College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China.,State Key Laboratory of Crop Biology, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China
| | - Qijie Wu
- College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China
| | - Xiude Chen
- College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China.,State Key Laboratory of Crop Biology, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China.,Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China
| | - Dongsheng Gao
- College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China. .,State Key Laboratory of Crop Biology, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China. .,Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China.
| | - Hongyu Wu
- College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China. .,State Key Laboratory of Crop Biology, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China. .,Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China.
| |
Collapse
|
25
|
A genome-wide association study identified loci for yield component traits in sugarcane (Saccharum spp.). PLoS One 2019; 14:e0219843. [PMID: 31318931 PMCID: PMC6638961 DOI: 10.1371/journal.pone.0219843] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 07/02/2019] [Indexed: 12/14/2022] Open
Abstract
Sugarcane (Saccharum spp.) has a complex genome with variable ploidy and frequent aneuploidy, which hampers the understanding of phenotype and genotype relations. Despite this complexity, genome-wide association studies (GWAS) may be used to identify favorable alleles for target traits in core collections and then assist breeders in better managing crosses and selecting superior genotypes in breeding populations. Therefore, in the present study, we used a diversity panel of sugarcane, called the Brazilian Panel of Sugarcane Genotypes (BPSG), with the following objectives: (i) estimate, through a mixed model, the adjusted means and genetic parameters of the five yield traits evaluated over two harvest years; (ii) detect population structure, linkage disequilibrium (LD) and genetic diversity using simple sequence repeat (SSR) markers; (iii) perform GWAS analysis to identify marker-trait associations (MTAs); and iv) annotate the sequences giving rise to SSR markers that had fragments associated with target traits to search for putative candidate genes. The phenotypic data analysis showed that the broad-sense heritability values were above 0.48 and 0.49 for the first and second harvests, respectively. The set of 100 SSR markers produced 1,483 fragments, of which 99.5% were polymorphic. These SSR fragments were useful to estimate the most likely number of subpopulations, found to be four, and the LD in BPSG, which was stronger in the first 15 cM and present to a large extension (65 cM). Genetic diversity analysis showed that, in general, the clustering of accessions within the subpopulations was in accordance with the pedigree information. GWAS performed through a multilocus mixed model revealed 23 MTAs, six, three, seven, four and three for soluble solid content, stalk height, stalk number, stalk weight and cane yield traits, respectively. These MTAs may be validated in other populations to support sugarcane breeding programs with introgression of favorable alleles and marker-assisted selection.
Collapse
|
26
|
Picarella ME, Mazzucato A. The Occurrence of Seedlessness in Higher Plants; Insights on Roles and Mechanisms of Parthenocarpy. FRONTIERS IN PLANT SCIENCE 2019; 9:1997. [PMID: 30713546 PMCID: PMC6345683 DOI: 10.3389/fpls.2018.01997] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 12/24/2018] [Indexed: 05/06/2023]
Abstract
Parthenocarpy in a broad sense includes those processes that allow the production of seedless fruits. Such fruits are favorable to growers, because they are set independently of successful pollination, and to processors and consumers, because they are easier to deal with and to eat. Seedless fruits however represent a biological paradox because they do not contribute to offspring production. In this work, the occurrence of parthenocarpy in Angiosperms was investigated by conducting a bibliographic survey. We distinguished monospermic (single seeded) from plurispermic (multiseeded) species and wild from cultivated taxa. Out of 96 seedless taxa, 66% belonged to plurispermic species. Of these, cultivated species were represented six times higher than wild species, suggesting a selective pressure for parthenocarpy during domestication and breeding. In monospermic taxa, wild and cultivated species were similarly represented. The occurrence of parthenocarpy in wild species suggests that seedlessness may have an adaptive role. In monospermic species, seedless fruits are proposed to reduce seed predation through deceptive mechanisms. In plurispermic fruit species, parthenocarpy may exert an adaptive advantage under suboptimal pollination regimes, when too few embryos are formed to support fruit growth. In this situation, parthenocarpy offers the opportunity to accomplish the production and dispersal of few seeds, thus representing a selective advantage. Approximately 20 sources of seedlessness have been described in tomato. Excluding the EMS induced mutation parthenocarpic fruit (pat), the parthenocarpic phenotype always emerged in biparental populations derived from wide crosses between cultivated tomato and wild relatives. Following a theory postulated for apomictic species, we argument that wide hybridization could also be the force driving parthenocarpy, following the disruption of synchrony in time and space of reproductive developmental events, from sporogenesis to fruit development. The high occurrence of polyploidy among parthenocarpic species supported this suggestion. Other commonalities between apomixis and parthenocarpy emerged from genetic and molecular studies of the two phenomena. Such insights may improve the understanding of the mechanisms underlying these two reproductive variants of great importance to modern breeding.
Collapse
Affiliation(s)
| | - Andrea Mazzucato
- Laboratory of Biotechnologies of Vegetable Crops, Department of Agriculture and Forest Sciences, University of Tuscia, Viterbo, Italy
| |
Collapse
|
27
|
Halewood M, Lopez Noriega I, Ellis D, Roa C, Rouard M, Sackville Hamilton R. Using Genomic Sequence Information to Increase Conservation and Sustainable Use of Crop Diversity and Benefit-Sharing. Biopreserv Biobank 2018; 16:368-376. [PMID: 30325667 PMCID: PMC6204560 DOI: 10.1089/bio.2018.0043] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
This article describes how CGIAR centers and partners are using genomic sequence information to promote the conservation and sustainable use of crop genetic diversity, and to generate and share benefits derived from those uses. The article highlights combined institutional, and benefit-sharing-related challenges that need to be addressed to support expanded use of digital sequence information in agricultural research and development.
Collapse
Affiliation(s)
| | | | - Dave Ellis
- 2 International Potato Center , Lima, Peru
| | - Carolina Roa
- 3 Centro Internacional de Agricultura Tropical , Cali, Colombia
| | | | | |
Collapse
|
28
|
Rouard M, Droc G, Martin G, Sardos J, Hueber Y, Guignon V, Cenci A, Geigle B, Hibbins MS, Yahiaoui N, Baurens FC, Berry V, Hahn MW, D’Hont A, Roux N. Three New Genome Assemblies Support a Rapid Radiation in Musa acuminata (Wild Banana). Genome Biol Evol 2018; 10:3129-3140. [PMID: 30321324 PMCID: PMC6282646 DOI: 10.1093/gbe/evy227] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/10/2018] [Indexed: 12/15/2022] Open
Abstract
Edible bananas result from interspecific hybridization between Musa acuminata and Musa balbisiana, as well as among subspecies in M. acuminata. Four particular M. acuminata subspecies have been proposed as the main contributors of edible bananas, all of which radiated in a short period of time in southeastern Asia. Clarifying the evolution of these lineages at a whole-genome scale is therefore an important step toward understanding the domestication and diversification of this crop. This study reports the de novo genome assembly and gene annotation of a representative genotype from three different subspecies of M. acuminata. These data are combined with the previously published genome of the fourth subspecies to investigate phylogenetic relationships. Analyses of shared and unique gene families reveal that the four subspecies are quite homogenous, with a core genome representing at least 50% of all genes and very few M. acuminata species-specific gene families. Multiple alignments indicate high sequence identity between homologous single copy-genes, supporting the close relationships of these lineages. Interestingly, phylogenomic analyses demonstrate high levels of gene tree discordance, due to both incomplete lineage sorting and introgression. This pattern suggests rapid radiation within Musa acuminata subspecies that occurred after the divergence with M. balbisiana. Introgression between M. a. ssp. malaccensis and M. a. ssp. burmannica was detected across the genome, though multiple approaches to resolve the subspecies tree converged on the same topology. To support evolutionary and functional analyses, we introduce the PanMusa database, which enables researchers to exploration of individual gene families and trees.
Collapse
Affiliation(s)
- Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, France
| | - Gaetan Droc
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, France
| | - Guillaume Martin
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, France
| | - Julie Sardos
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, France
| | - Yann Hueber
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, France
| | - Valentin Guignon
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, France
| | - Alberto Cenci
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, France
| | | | - Mark S Hibbins
- Department of Biology, Indiana University
- Department of Computer Science, Indiana University
| | - Nabila Yahiaoui
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, France
| | - Franc-Christophe Baurens
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, France
| | - Vincent Berry
- LIRMM, Université de Montpellier, CNRS, Montpellier, France
| | - Matthew W Hahn
- Department of Biology, Indiana University
- Department of Computer Science, Indiana University
| | - Angelique D’Hont
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, France
| | - Nicolas Roux
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, France
| |
Collapse
|
29
|
Halewood M, Chiurugwi T, Sackville Hamilton R, Kurtz B, Marden E, Welch E, Michiels F, Mozafari J, Sabran M, Patron N, Kersey P, Bastow R, Dorius S, Dias S, McCouch S, Powell W. Plant genetic resources for food and agriculture: opportunities and challenges emerging from the science and information technology revolution. THE NEW PHYTOLOGIST 2018; 217:1407-1419. [PMID: 29359808 DOI: 10.1111/nph.14993] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 11/21/2017] [Indexed: 05/21/2023]
Abstract
Contents Summary 1407 I. Introduction 1408 II. Technological advances and their utility for gene banks and breeding, and longer-term contributions to SDGs 1408 III. The challenges that must be overcome to realise emerging R&D opportunities 1410 IV. Renewed governance structures for PGR (and related big data) 1413 V. Access and benefit sharing and big data 1416 VI. Conclusion 1417 Acknowledgements 1417 ORCID 1417 References 1417 SUMMARY: Over the last decade, there has been an ongoing revolution in the exploration, manipulation and synthesis of biological systems, through the development of new technologies that generate, analyse and exploit big data. Users of Plant Genetic Resources (PGR) can potentially leverage these capacities to significantly increase the efficiency and effectiveness of their efforts to conserve, discover and utilise novel qualities in PGR, and help achieve the Sustainable Development Goals (SDGs). This review advances the discussion on these emerging opportunities and discusses how taking advantage of them will require data integration and synthesis across disciplinary, organisational and international boundaries, and the formation of multi-disciplinary, international partnerships. We explore some of the institutional and policy challenges that these efforts will face, particularly how these new technologies may influence the structure and role of research for sustainable development, ownership of resources, and access and benefit sharing. We discuss potential responses to political and institutional challenges, ranging from options for enhanced structure and governance of research discovery platforms to internationally brokered benefit-sharing agreements, and identify a set of broad principles that could guide the global community as it seeks or considers solutions.
Collapse
Affiliation(s)
- Michael Halewood
- Bioversity International, Via dei Tre Denari, 472/a, 00054, Maccarese, Rome, Italy
| | | | - Ruaraidh Sackville Hamilton
- T. T. Chang Genetic Resources Center, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Brad Kurtz
- Independent Crop Biodiversity and Intellectual Property Expert, 25057 River Ridge Road, Adel, IA, 50003, USA
| | - Emily Marden
- University of British Columbia, Peter A. Allard School of Law, 1822 East Mall, Vancouver, BC, V6T 1Z1, Canada
| | - Eric Welch
- School of Public Affairs, College of Public Programs, Arizona State University, 411 North Central Avenue, Suite 463, Phoenix, AZ, 85004-0687, USA
| | - Frank Michiels
- Independent Crop Biodiversity and Intellectual Property Expert, Technologiepark 38, 9052, Gent, Belgium
| | - Javad Mozafari
- Agricultural Research, Education and Extension Organization, Yemen St., Chamran Freeway, Tehran, Iran
| | - Muhamad Sabran
- Indonesian Centre for Biotechnology and Genetic Resources, JL Tentara Pelajar No. 3A, Kampus Penelitian Pertanian Cimanggu, Bogor, 16111, Indonesia
| | - Nicola Patron
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Paul Kersey
- EMBL -The European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Ruth Bastow
- Global Plant Council, Bow House, 1a Bow Lane, London, EC4M 9EE, UK
| | - Shawn Dorius
- Department of Sociology, Iowa State University, 308 East Hall, Ames, IA, 50010, USA
| | - Sonia Dias
- Secretariat of International Treaty on Plant Genetic Resources for Food and Agriculture, Viale delle Terme di Caracalla, 00153, Rome, Italy
| | - Susan McCouch
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, 240 Emerson Hall, Ithaca, NY, 14853, USA
| | - Wayne Powell
- SRUC (Scotland's Rural College), Peter Wilson Building, West Mains Road, Edinburgh, EH9 3JG, UK
| |
Collapse
|
30
|
Joldersma D, Liu Z. The making of virgin fruit: the molecular and genetic basis of parthenocarpy. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:955-962. [PMID: 29325151 PMCID: PMC6018997 DOI: 10.1093/jxb/erx446] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 11/25/2017] [Indexed: 05/16/2023]
Abstract
Fruit set-the commitment of an angiosperm plant to develop fruit-is a key developmental process that normally occurs following successful fertilization. Parthenocarpy arises when fruit automatically develop in the absence of fertilization. This review uses parthenocarpic fruit development as a focal device through which to recapitulate and understand the molecular effectors that mediate and regulate fruit set. The review demonstrates that studies of parthenocarpy are providing vital insight into plant development, signaling and, potentially, high-value agricultural products.
Collapse
Affiliation(s)
- Dirk Joldersma
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | - Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
- Correspondence:
| |
Collapse
|
31
|
Ruas M, Guignon V, Sempere G, Sardos J, Hueber Y, Duvergey H, Andrieu A, Chase R, Jenny C, Hazekamp T, Irish B, Jelali K, Adeka J, Ayala-Silva T, Chao CP, Daniells J, Dowiya B, Effa Effa B, Gueco L, Herradura L, Ibobondji L, Kempenaers E, Kilangi J, Muhangi S, Ngo Xuan P, Paofa J, Pavis C, Thiemele D, Tossou C, Sandoval J, Sutanto A, Vangu Paka G, Yi G, Van den Houwe I, Roux N, Rouard M. MGIS: managing banana (Musa spp.) genetic resources information and high-throughput genotyping data. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2017:3866796. [PMID: 29220435 PMCID: PMC5502358 DOI: 10.1093/database/bax046] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 05/12/2017] [Indexed: 12/22/2022]
Abstract
Unraveling the genetic diversity held in genebanks on a large scale is underway, due to advances in Next-generation sequence (NGS) based technologies that produce high-density genetic markers for a large number of samples at low cost. Genebank users should be in a position to identify and select germplasm from the global genepool based on a combination of passport, genotypic and phenotypic data. To facilitate this, a new generation of information systems is being designed to efficiently handle data and link it with other external resources such as genome or breeding databases. The Musa Germplasm Information System (MGIS), the database for global ex situ-held banana genetic resources, has been developed to address those needs in a user-friendly way. In developing MGIS, we selected a generic database schema (Chado), the robust content management system Drupal for the user interface, and Tripal, a set of Drupal modules which links the Chado schema to Drupal. MGIS allows germplasm collection examination, accession browsing, advanced search functions, and germplasm orders. Additionally, we developed unique graphical interfaces to compare accessions and to explore them based on their taxonomic information. Accession-based data has been enriched with publications, genotyping studies and associated genotyping datasets reporting on germplasm use. Finally, an interoperability layer has been implemented to facilitate the link with complementary databases like the Banana Genome Hub and the MusaBase breeding database. Database URL:https://www.crop-diversity.org/mgis/
Collapse
Affiliation(s)
- Max Ruas
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - V Guignon
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France.,South Green Bioinformatics Platform, Montpellier, France
| | - G Sempere
- South Green Bioinformatics Platform, Montpellier, France.,CIRAD, UMR AGAP 34398 Montpellier Cedex 5, France
| | - J Sardos
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - Y Hueber
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France.,South Green Bioinformatics Platform, Montpellier, France
| | - H Duvergey
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - A Andrieu
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - R Chase
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - C Jenny
- CIRAD, UMR AGAP 34398 Montpellier Cedex 5, France
| | - T Hazekamp
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - B Irish
- USDA-ARS-Tropical Agriculture Research Station, Mayaguez, Puerto Rico
| | - K Jelali
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - J Adeka
- University of Kisangani, Kisangani (UNIKIS), Democratic Republic of Congo
| | - T Ayala-Silva
- USDA-ARS-Tropical Agriculture Research Station, Mayaguez, Puerto Rico
| | - C P Chao
- Taiwan Banana Research Institute (TBRI), Chiuju, Pingtung, Taiwan, Republic of China
| | - J Daniells
- Department of Agriculture, Fisheries and Forestry, Queensland Government (DAFF South Johnstone), Brisbane, Australia
| | - B Dowiya
- Institut National pour l'Etude et la Recherche Agronomiques (INERA), Democratic Republic of Congo
| | - B Effa Effa
- Centre National de la Recherche Scientifique et Technologique (CENAREST), Libreville, Gabon
| | - L Gueco
- Institute of Plant Breeding (IPB), University of the Philippines (UPLB), Los Baños, Philippines
| | - L Herradura
- Bureau of Plant Industry (BPI) - Davao National Crop Research and Development Center, Davao City, Philippines
| | - L Ibobondji
- Centre Africain de Recherche sur Bananes et Plantains (CARBAP), Njombe, Cameroon
| | - E Kempenaers
- Bioversity International, International Musa Germplasm Transit Center (ITC), KULeuven, Leuven, Belgium
| | - J Kilangi
- Agricultural Research Institute (ARI) Maruku, Bukoba, Tanzania
| | - S Muhangi
- National Agricultural Research Organization (NARO), Mbarara, Uganda
| | - P Ngo Xuan
- Fruit and Vegetable Research Institute (FAVRI), Hanoi, Vietnam
| | - J Paofa
- National Agricultural Research Institute (NARI), Laloki Papua, New Guinea
| | - C Pavis
- CRB Plantes Tropicales, CIRAD INRA - Neufchâteau, Guadeloupe, France
| | - D Thiemele
- Centre National de Recherches Agronomiques (CNRA), Abidjan, Cote d'Ivoire
| | - C Tossou
- Institut National de Recherche Agronomique du Bénin (INRAB), Cotonou, Bénin
| | - J Sandoval
- Corporación Bananera Nacional S.A (CORBANA), San José, Costa Rica
| | - A Sutanto
- Indonesian Centre for Horticultural Research and Development (ICHORD), Bogor, Indonesia
| | - G Vangu Paka
- Institut National pour l'Etude et la Recherche Agronomiques (INERA), Democratic Republic of Congo
| | - G Yi
- Institute of Fruit Tree Research (IFTR), Guangdong Academy of Agricultural Sciences (GDAAS), Guangdong, China
| | - I Van den Houwe
- Bioversity International, International Musa Germplasm Transit Center (ITC), KULeuven, Leuven, Belgium
| | - N Roux
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France.,Bioversity International, International Musa Germplasm Transit Center (ITC), KULeuven, Leuven, Belgium
| | - M Rouard
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France.,South Green Bioinformatics Platform, Montpellier, France
| |
Collapse
|
32
|
van Wesemael J, Hueber Y, Kissel E, Campos N, Swennen R, Carpentier S. Homeolog expression analysis in an allotriploid non-model crop via integration of transcriptomics and proteomics. Sci Rep 2018; 8:1353. [PMID: 29358676 PMCID: PMC5777989 DOI: 10.1038/s41598-018-19684-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 01/08/2018] [Indexed: 01/14/2023] Open
Abstract
The fate of doubled genes, from allopolyploid or autopolyploid origin, is controlled at multiple levels, resulting in the modern day cultivars. We studied the root growth of 3 different triploid banana cultivars under control and osmotic stress conditions. The root growth of the allopolyploid ABB cultivar was 42% higher under control and 61% higher under osmotic stress. By integrating transcriptomics and proteomics, we studied the gene expression of all 3 cultivars, resulting in 2,749 identified root proteins. 383 gene loci displayed genotype specific differential expression whereof 252 showed at least one Single Amino Acid Polymorphism (SAAP). In the ABB cultivar, allele expressions supposedly follow a 1/3 and 2/3 pattern for respectively the A and the B allele. Using transcriptome read alignment to assess the homeoallelic contribution we found that 63% of the allele specific genes deviated from this expectation. 32 gene loci even did not express the A allele. The identified ABB allele- specific proteins correlate well with the observed growth phenotype as they are enriched in energy related functions such as ATP metabolic processes, nicotinamide nucleotide metabolic processes, and glycolysis.
Collapse
Affiliation(s)
- Jelle van Wesemael
- Laboratory of Tropical Crop Improvement, KU Leuven, Willem Decroylaan 42, Leuven, Belgium
| | - Yann Hueber
- Bioversity International, Parc Scientifique Argropolis II, Montpellier, France
| | - Ewaut Kissel
- Laboratory of Tropical Crop Improvement, KU Leuven, Willem Decroylaan 42, Leuven, Belgium
| | - Nádia Campos
- Laboratory of Tropical Crop Improvement, KU Leuven, Willem Decroylaan 42, Leuven, Belgium
| | - Rony Swennen
- Laboratory of Tropical Crop Improvement, KU Leuven, Willem Decroylaan 42, Leuven, Belgium
- Bioversity International, Willem Decroylaan 42, Leuven, Belgium
- International Institute for Tropical Agriculture, C/O Nelson Mandela Institute of Science and technology, P.O. Box 44, Arusha, Tanzania
| | - Sebastien Carpentier
- Laboratory of Tropical Crop Improvement, KU Leuven, Willem Decroylaan 42, Leuven, Belgium.
- Bioversity International, Willem Decroylaan 42, Leuven, Belgium.
- Facility for SYstems BIOlogy based MAss spectrometry, Herestraat 49, Leuven, Belgium.
| |
Collapse
|
33
|
Dash PK, Rai R. Translating the "Banana Genome" to Delineate Stress Resistance, Dwarfing, Parthenocarpy and Mechanisms of Fruit Ripening. FRONTIERS IN PLANT SCIENCE 2016; 7:1543. [PMID: 27833619 PMCID: PMC5080353 DOI: 10.3389/fpls.2016.01543] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Accepted: 09/30/2016] [Indexed: 05/07/2023]
Abstract
Evolutionary frozen, genetically sterile and globally iconic fruit "Banana" remained untouched by the green revolution and, as of today, researchers face intrinsic impediments for its varietal improvement. Recently, this wonder crop entered the genomics era with decoding of structural genome of double haploid Pahang (AA genome constitution) genotype of Musa acuminata. Its complex genome decoded by hybrid sequencing strategies revealed panoply of genes and transcription factors involved in the process of sucrose conversion that imparts sweetness to its fruit. Historically, banana has faced the wrath of pandemic bacterial, fungal, and viral diseases and multitude of abiotic stresses that has ruined the livelihood of small/marginal farmers' and destroyed commercial plantations. Decoding structural genome of this climacteric fruit has given impetus to a deeper understanding of the repertoire of genes involved in disease resistance, understanding the mechanism of dwarfing to develop an ideal plant type, unraveling the process of parthenocarpy, and fruit ripening for better fruit quality. Further, injunction of comparative genomics will usher in integration of information from its decoded genome and other monocots into field applications in banana related but not limited to yield enhancement, food security, livelihood assurance, and energy sustainability. In this mini review, we discuss pre- and post-genomic discoveries and highlight accomplishments in structural genomics, genetic engineering and forward genetic accomplishments with an aim to target genes and transcription factors for translational research in banana.
Collapse
Affiliation(s)
- Prasanta K. Dash
- ICAR-National Research Centre on Plant BiotechnologyNew Delhi, India
| | | |
Collapse
|