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Liu J, Magige EA, Fan PZ, Wambulwa MC, Luo YH, Qi HL, Gao LM, Milne RI. Genetic imprints of grafting in wild iron walnut populations in southwestern China. BMC PLANT BIOLOGY 2023; 23:423. [PMID: 37700228 PMCID: PMC10498525 DOI: 10.1186/s12870-023-04428-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 08/29/2023] [Indexed: 09/14/2023]
Abstract
BACKGROUND Anthropogenic activities are causing unprecedented loss of genetic diversity in many species. However, the effects on genetic diversity from large-scale grafting onto wild plants of crop species are largely undetermined. Iron walnut (Juglans sigillata Dode) is a deciduous nut tree crop endemic to southwestern China with a long history of cultivation. Due to the rapid expansion of the walnut industry, many natural populations are now being replaced by cultivars grafted onto wild rootstocks. However, little is known about the potential genetic consequences of such action on natural populations. RESULTS We sampled the scion and the rootstock from each of 149 grafted individuals within nine wild populations of J. sigillata from Yunnan Province which is the center of walnut diversity and cultivation in China, and examined their genetic diversity and population structure using 31 microsatellite loci. Scions had lower genetic diversity than rootstocks, and this pattern was repeated in seven of the nine examined populations. Among those seven populations, AMOVA and clustering analyses showed a clear genetic separation between all rootstocks and all scions. However, the two remaining populations, both from northern Yunnan, showed genetic similarity between scions and rootstocks, possibly indicating that wild populations here are derived from feralized local cultivars. Moreover, our data indicated probable crop-to-wild gene flow between scions and rootstocks, across all populations. CONCLUSIONS Our results indicate that large-scale grafting has been causing genetic diversity erosion and genetic structure breakdown in the wild material of J. sigillata within Yunnan. To mitigate these effects, we caution against the overuse of grafting in wild populations of iron walnut and other crop species and recommend the preservation of natural genotypes through in situ and ex situ conservation.
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Affiliation(s)
- Jie Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China.
- Germplasm of Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China.
| | - Ephie A Magige
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- Germplasm of Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Peng-Zhen Fan
- Germplasm of Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Moses C Wambulwa
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- Germplasm of Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- Department of Life Sciences, School of Science and Computing, South Eastern Kenya University, Kitui, 170-90200, Kenya
| | - Ya-Huang Luo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- Germplasm of Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- Lijiang Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, Yunnan, 674100, China
| | - Hai-Ling Qi
- School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, 650091, China
| | - Lian-Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China.
- Germplasm of Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China.
- Lijiang Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, Yunnan, 674100, China.
| | - Richard I Milne
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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Wambulwa MC, Fan PZ, Milne R, Wu ZY, Luo YH, Wang YH, Wang H, Gao LM, Xiahou ZY, Jin YC, Ye LJ, Xu ZC, Yang ZC, Li DZ, Liu J. Genetic analysis of walnut cultivars from southwest China: Implications for germplasm improvement. PLANT DIVERSITY 2022; 44:530-541. [PMID: 36540707 PMCID: PMC9751080 DOI: 10.1016/j.pld.2021.08.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/26/2021] [Accepted: 08/18/2021] [Indexed: 05/19/2023]
Abstract
Walnuts are highly valued for their rich nutritional profile and wide medicinal applications. This demand has led to the intensification of breeding activities in major walnut production areas such as southwest China, in order to develop more superior cultivars. With the increasing number of cultivars, accurate identification becomes fundamental to selecting the right cultivar for grafting, industrial processing or development of new cultivars. To ensure proper identification of cultivars and understand the genetic structure of wild and cultivated material, we genotyped 362 cultivated and wild individuals of walnut trees from southwest China (with two additional populations from Xinjiang, plus three cultivars from Canada, France and Belgium) using 36 polymorphic microsatellite loci. We found relatively low indices of genetic diversity (H O = 0.570, H E = 0.404, N A = 2.345) as well as a high level of clonality (>85% of cultivars), indicating reliance on genetically narrow sources of parental material for breeding. Our STRUCTURE and PCoA analyses generally delineated the two species, though considerable levels of introgression were also evident. More significantly, we detected a distinct genetic group of cultivated Juglans sigillata, which mainly comprised individuals of the popular 'Yangbidapao' landrace. Finally, a core set of 18 SSR loci was selected, which was capable of identifying 32 cultivars. In a nutshell, our results call for more utilization of genetically disparate material, including wild walnut trees, as parental sources to breed for more cultivars. The data reported herein will significantly contribute towards the genetic improvement and conservation of the walnut germplasm in southwest China.
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Affiliation(s)
- Moses C. Wambulwa
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Department of Life Sciences, South Eastern Kenya University, 170-90200, Kitui, Kenya
| | - Peng-Zhen Fan
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Richard Milne
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Zeng-Yuan Wu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Ya-Huang Luo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Yue-Hua Wang
- School of School of Ecology and Environmental Science, Yunnan University, Kunming, 650091, Yunnan, China
| | - Hong Wang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Lian-Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Zuo-Ying Xiahou
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Ye-Chuan Jin
- School of School of Ecology and Environmental Science, Yunnan University, Kunming, 650091, Yunnan, China
| | - Lin-Jiang Ye
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Zu-Chang Xu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Zhi-Chun Yang
- Yangbi Forestry and Grassland Administration, Dali, 672500, Yunnan, China
| | - De-Zhu Li
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- College of Life Sciences, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Corresponding author. Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Jie Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Corresponding author. CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
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Magige EA, Fan PZ, Wambulwa MC, Milne R, Wu ZY, Luo YH, Khan R, Wu HY, Qi HL, Zhu GF, Maity D, Khan I, Gao LM, Liu J. Genetic Diversity and Structure of Persian Walnut (Juglans regia L.) in Pakistan: Implications for Conservation. PLANTS 2022; 11:plants11131652. [PMID: 35807604 PMCID: PMC9269025 DOI: 10.3390/plants11131652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/08/2022] [Accepted: 06/18/2022] [Indexed: 12/02/2022]
Abstract
Persian (Common) walnut (Juglans regia L.) is a famous fruit tree species valued for its nutritious nuts and high-quality wood. Although walnut is widely distributed and plays an important role in the economy and culture of Pakistan, the genetic diversity and structure of its populations in the country remains poorly understood. Therefore, using 31 nuclear microsatellites, we assessed the genetic diversity and population structure of 12 walnut populations sampled across Pakistan. We also implemented the geostatistical IDW technique in ArcGIS to reveal “hotspots” of genetic diversity. Generally, the studied populations registered relatively low indices of genetic diversity (NA = 3.839, HO = 0.558, UHE = 0.580), and eight populations had positive inbreeding coefficient (FIS) values. Low among-population differentiation was indicated by AMOVA, pairwise FST and DC. STRUCTURE, PCoA and neighbor joining (NJ) analysis revealed a general lack of clear clustering in the populations except that one population in Upper Dir was clearly genetically distinct from the rest. Furthermore, the Mantel test showed no correlation between the geographic and genetic distance (r = 0.14, p = 0.22), while barrier analysis suggested three statistically significant genetic barriers. Finally, the spatial interpolation results indicated that populations in Ziarat, Kashmir, Dir, Swat, Chitral, and upper Dir had high intrapopulation genetic diversity, suggesting the need to conserve populations in those areas. The results from this study will be important for future breeding improvement and conservation of walnuts in Pakistan.
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Affiliation(s)
- Ephie A. Magige
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (E.A.M.); (M.C.W.); (Z.-Y.W.); (Y.-H.L.); (H.-Y.W.)
- Germplasm of Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (P.-Z.F.); (G.-F.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peng-Zhen Fan
- Germplasm of Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (P.-Z.F.); (G.-F.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Moses C. Wambulwa
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (E.A.M.); (M.C.W.); (Z.-Y.W.); (Y.-H.L.); (H.-Y.W.)
- Germplasm of Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (P.-Z.F.); (G.-F.Z.)
- Department of Life Sciences, School of Science and Computing, South Eastern Kenya University, Kitui 170-90200, Kenya
| | - Richard Milne
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JH, UK;
| | - Zeng-Yuan Wu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (E.A.M.); (M.C.W.); (Z.-Y.W.); (Y.-H.L.); (H.-Y.W.)
- Germplasm of Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (P.-Z.F.); (G.-F.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ya-Huang Luo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (E.A.M.); (M.C.W.); (Z.-Y.W.); (Y.-H.L.); (H.-Y.W.)
- Germplasm of Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (P.-Z.F.); (G.-F.Z.)
| | - Raees Khan
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia;
| | - Hong-Yu Wu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (E.A.M.); (M.C.W.); (Z.-Y.W.); (Y.-H.L.); (H.-Y.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hai-Ling Qi
- School of Ecology and Environmental Science, Yunnan University, Kunming 650091, China;
| | - Guang-Fu Zhu
- Germplasm of Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (P.-Z.F.); (G.-F.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Debabrata Maity
- Department of Botany, University of Calcutta, Kolkata 700019, India;
| | - Ikramullah Khan
- Department of Botany, Abdul Wali Khan University Mardan, KP, Mardan 23200, Pakistan;
| | - Lian-Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (E.A.M.); (M.C.W.); (Z.-Y.W.); (Y.-H.L.); (H.-Y.W.)
- Germplasm of Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (P.-Z.F.); (G.-F.Z.)
- Lijiang Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang 674100, China
- Correspondence: (L.-M.G.); (J.L.)
| | - Jie Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (E.A.M.); (M.C.W.); (Z.-Y.W.); (Y.-H.L.); (H.-Y.W.)
- Germplasm of Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (P.-Z.F.); (G.-F.Z.)
- Correspondence: (L.-M.G.); (J.L.)
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Ramadoss N, Orduño-Baez A, Portillo C, Steele S, Rebman J, Flores-Rentería L. Unraveling the development behind unisexual flowers in Cylindropuntia wolfii (Cactaceae). BMC PLANT BIOLOGY 2022; 22:94. [PMID: 35236303 PMCID: PMC8889693 DOI: 10.1186/s12870-022-03431-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 01/07/2022] [Indexed: 05/31/2023]
Abstract
BACKGROUND In certain unisexual flowers, non-functional sexual organs remain vestigial and unisexuality can be overlooked leading to the ambiguous description of the sexual systems. Therefore, to accurately describe the sexual system, detailed morphological and developmental analyses along with experimental crosses must be performed. Cylindropuntia wolfii is a rare cactus endemic to the Sonoran Desert in southern California and northern Baja California that was described as gynodioecious by morphological analysis. The aims of our project include accurately identifying the sexual system of C. wolfii using histological and functional studies and characterizing the developmental mechanisms that underlie its floral development. METHODS Histological analyses were carried out on different stages of C. wolfii flowers and controlled crosses were performed in the field. RESULT Our results identified C. wolfii to be functionally dioecious. The ovule and anther development differed between staminate and pistillate flowers. In vivo pollen germination tests showed that the pollen of staminate and pistillate flowers were viable and the stigma and style of both staminate and pistillate flowers were receptive. This suggests that there are no genetic or developmental barriers in the earlier stages of pollen recognition and pollen germination. CONCLUSIONS Despite being functionally dioecious, we observed that functionally pistillate individuals produced fruits with a large number of aborted seeds. This implies that not only does this species have low reproductive success, but its small population sizes may lead to low genetic diversity.
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Affiliation(s)
| | - Amy Orduño-Baez
- Department of Biology, San Diego State University, San Diego, USA
- University of Santa Cruz, San Diego, USA
| | - Carlos Portillo
- Department of Biology, San Diego State University, San Diego, USA
| | - Scarlet Steele
- Department of Biology, San Diego State University, San Diego, USA
| | - Jon Rebman
- Department of Botany, San Diego Natural History Museum, San Diego, USA
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Pavan S, Delvento C, Mazzeo R, Ricciardi F, Losciale P, Gaeta L, D'Agostino N, Taranto F, Sánchez-Pérez R, Ricciardi L, Lotti C. Almond diversity and homozygosity define structure, kinship, inbreeding, and linkage disequilibrium in cultivated germplasm, and reveal genomic associations with nut and seed weight. HORTICULTURE RESEARCH 2021; 8:15. [PMID: 33423037 PMCID: PMC7797004 DOI: 10.1038/s41438-020-00447-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 11/04/2020] [Accepted: 11/13/2020] [Indexed: 05/04/2023]
Abstract
Almond [Prunus dulcis Miller (D.A. Webb)] is the main tree nut species worldwide. Here, genotyping-by-sequencing (GBS) was applied to 149 almond cultivars from the ex situ collections of the Italian Council for Agricultural Research (CREA) and the Spanish National Research Council (CSIC), leading to the detection of 93,119 single-nucleotide polymorphisms (SNPs). The study of population structure outlined four distinct genetic groups and highlighted diversification between the Mediterranean and Californian gene pools. Data on SNP diversity and runs of homozygosity (ROHs) allowed the definition of kinship, inbreeding, and linkage disequilibrium (LD) decay in almond cultivated germplasm. Four-year phenotypic observations, gathered on 98 cultivars of the CREA collection, were used to perform a genome-wide association study (GWAS) and, for the first time in a crop species, homozygosity mapping (HM), resulting in the identification of genomic associations with nut, shell, and seed weight. Both GWAS and HM suggested that loci controlling nut and seed weight are mostly independent. Overall, this study provides insights on the almond cultivation history and delivers information of major interest for almond genetics and breeding. In a broader perspective, our results encourage the use of ROHs in crop science to estimate inbreeding, choose parental combinations minimizing the risk of inbreeding depression, and identify genomic footprints of selection for specific traits.
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Affiliation(s)
- Stefano Pavan
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Via Amendola 165/A, Bari, 70126, Italy.
- Institute of Biomedical Technologies, National Research Council (CNR), Via Amendola 122/D, Bari, 70126, Italy.
| | - Chiara Delvento
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Via Amendola 165/A, Bari, 70126, Italy
| | - Rosa Mazzeo
- Department of the Sciences of Agriculture, Food and Environment, University of Foggia, Via Napoli 25, Foggia, 71100, Italy
| | - Francesca Ricciardi
- Department of the Sciences of Agriculture, Food and Environment, University of Foggia, Via Napoli 25, Foggia, 71100, Italy
| | - Pasquale Losciale
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Via Amendola 165/A, Bari, 70126, Italy
| | - Liliana Gaeta
- Council for Agricultural Research and Economics-Research Centre for Agriculture and Environment (CREA-AA), Bari, 70125, Italy
| | - Nunzio D'Agostino
- Department of Agricultural Sciences, University of Naples Federico II, Portici, 80055, Italy
| | - Francesca Taranto
- Institute of Biosciences and Bioresources, National Research Council of Italy, Portici, 80055, Italy
| | | | - Luigi Ricciardi
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Via Amendola 165/A, Bari, 70126, Italy
| | - Concetta Lotti
- Department of the Sciences of Agriculture, Food and Environment, University of Foggia, Via Napoli 25, Foggia, 71100, Italy.
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Pérez de Los Cobos F, Martínez-García PJ, Romero A, Miarnau X, Eduardo I, Howad W, Mnejja M, Dicenta F, Socias I Company R, Rubio-Cabetas MJ, Gradziel TM, Wirthensohn M, Duval H, Holland D, Arús P, Vargas FJ, Batlle I. Pedigree analysis of 220 almond genotypes reveals two world mainstream breeding lines based on only three different cultivars. HORTICULTURE RESEARCH 2021; 8:11. [PMID: 33384415 PMCID: PMC7775440 DOI: 10.1038/s41438-020-00444-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 11/04/2020] [Accepted: 11/13/2020] [Indexed: 05/16/2023]
Abstract
Loss of genetic variability is an increasing challenge in tree breeding programs due to the repeated use of a reduced number of founder genotypes. However, in almond, little is known about the genetic variability in current breeding stocks, although several cases of inbreeding depression have been reported. To gain insights into the genetic structure in modern breeding programs worldwide, marker-verified pedigree data of 220 almond cultivars and breeding selections were analyzed. Inbreeding coefficients, pairwise relatedness, and genetic contribution were calculated for these genotypes. The results reveal two mainstream breeding lines based on three cultivars: "Tuono", "Cristomorto", and "Nonpareil". Descendants from "Tuono" or "Cristomorto" number 76 (sharing 34 descendants), while "Nonpareil" has 71 descendants. The mean inbreeding coefficient of the analyzed genotypes was 0.041, with 14 genotypes presenting a high inbreeding coefficient, over 0.250. Breeding programs from France, the USA, and Spain showed inbreeding coefficients of 0.075, 0.070, and 0.037, respectively. According to their genetic contribution, modern cultivars from Israel, France, the USA, Spain, and Australia trace back to a maximum of six main founding genotypes. Among the group of 65 genotypes carrying the Sf allele for self-compatibility, the mean relatedness coefficient was 0.125, with "Tuono" as the main founding genotype (24.7% of total genetic contribution). The results broaden our understanding about the tendencies followed in almond breeding over the last 50 years and will have a large impact into breeding decision-making process worldwide. Increasing current genetic variability is required in almond breeding programs to assure genetic gain and continuing breeding progress.
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Affiliation(s)
- Felipe Pérez de Los Cobos
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Mas Bové, Ctra. Reus-El Morell Km 3,8, 43120, Constantí, Tarragona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de Recerca en Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB. Cerdanyola del Vallès (Bellaterra), 08193, Barcelona, Spain
| | - Pedro J Martínez-García
- Centro de Edafología y Biología Aplicada del Segura, Consejo Superior de Investigaciones Científicas (CEBAS-CSIC), P.O. Box 164, 30100, Espinardo, Murcia, Spain
| | - Agustí Romero
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Mas Bové, Ctra. Reus-El Morell Km 3,8, 43120, Constantí, Tarragona, Spain
| | - Xavier Miarnau
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Fruitcentre, PCiTAL, Gardeny Park, Fruitcentre Building, 25003, Lleida, Spain
| | - Iban Eduardo
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de Recerca en Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB. Cerdanyola del Vallès (Bellaterra), 08193, Barcelona, Spain
| | - Werner Howad
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de Recerca en Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB. Cerdanyola del Vallès (Bellaterra), 08193, Barcelona, Spain
| | - Mourad Mnejja
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de Recerca en Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB. Cerdanyola del Vallès (Bellaterra), 08193, Barcelona, Spain
| | - Federico Dicenta
- Centro de Edafología y Biología Aplicada del Segura, Consejo Superior de Investigaciones Científicas (CEBAS-CSIC), P.O. Box 164, 30100, Espinardo, Murcia, Spain
| | - Rafel Socias I Company
- Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Avda. Montañana 930, 50059, Zaragoza, Instituto Agroalimentario de Aragón IA2 (CITA-Universidad de Zaragoza), Zaragoza, Spain
| | - Maria J Rubio-Cabetas
- Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Avda. Montañana 930, 50059, Zaragoza, Instituto Agroalimentario de Aragón IA2 (CITA-Universidad de Zaragoza), Zaragoza, Spain
| | | | - Michelle Wirthensohn
- University of Adelaide, Waite Research, School of Agriculture, Food and Wine, PMB 1, Glen Osmond, Adelaide, SA, 5064, Australia
| | - Henri Duval
- Institut National de la Recherche Agronomique (INRA), Domain St. Maurice CS 60094, 84143, Montfavet Cedex, France
| | - Doron Holland
- Agricultural Research Organization, Newe-Ya'ar Research Center, P.O. Box 1021, Ramat Yishad, 30095, Israel
| | - Pere Arús
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de Recerca en Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB. Cerdanyola del Vallès (Bellaterra), 08193, Barcelona, Spain
| | - Francisco J Vargas
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Mas Bové, Ctra. Reus-El Morell Km 3,8, 43120, Constantí, Tarragona, Spain
| | - Ignasi Batlle
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Mas Bové, Ctra. Reus-El Morell Km 3,8, 43120, Constantí, Tarragona, Spain.
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Using genetic markers to identify the origin of illegally traded agarwood-producing Aquilaria sinensis trees. Glob Ecol Conserv 2020. [DOI: 10.1016/j.gecco.2020.e00958] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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