|
Special Issue:
园艺-分子生物合辑Horticulture — Genetics · Breeding
|
|
|
|
| Analysis of genetic diversity and structure across a wide range of germplasm reveals genetic relationships among seventeen species of Malus Mill. native to China |
| GAO Yuan, WANG Da-jiang, WANG Kun, CONG Pei-hua, LI Lian-wen, PIAO Ji-cheng |
| Research Institute of Pomology, Chinese Academy of Agricultural Sciences/Key Laboratory of Horticultural Crops Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Xingcheng 125100, P.R.China |
|
|
|
|
摘要
中国是世界苹果属植物遗传多样性中心，中国原产苹果属植物有17个野生种和6个栽培种。利用19对SSR引物，对来源于14个省分属于17个种(12个野生种和5个栽培种)的798份苹果属植物材料进行鉴定评价。统计分析结果表明，798份种质具有较高的遗传多样性水平，其有效等位基因数(Ne)、期望杂合度(He)和香农信息指数(I)分别为10.309、0.886和2.545. 新疆野苹果 (He=0.814, I=2.041, Ne=6.054)、山荆子(He=0.848, I=2.350, Ne=8.652)、变叶海棠 (He=0.663, I=1.355, Ne=3.332) 和湖北海棠 (He=0.539, I=0.912, Ne=0.579) 的遗传多样性水平高于前人研究结果。新疆野苹果和山荆子只对部分中国苹果种质的起源演化有贡献，但是其他中国苹果种质却与山荆子和栽培种有更近的关系，尤其是八棱海棠、花红和楸子。并非所有的中国苹果种质均是由中国新疆的新疆野苹果演化而来。本研究为明确中国原产苹果属植物的亲缘关系提供新的理论依据，对解析苹果属植物遗传关系、种质资源保护和育种利用具有重要意义。
Abstract China is a center of diversity for Malus Mill. with 27 native species including 21 wild species and six domesticated species. We applied a set of 19 simple sequence repeat markers to genotype 798 accessions of 17 species (12 wild species and five cultivated species) of Malus originating from 14 provinces in China. A total of 500 alleles were detected. Diversity statistics indicated a high level of genetic variation as quantified by the average values of the effective allele number (Ne), expected heterozygosity (He), and Shannon’s Information Index (I) (10.309, 0.886, and 2.545, respectively). Malus sieversii (MSR; He=0.814, I=2.041, Ne=6.054), M. baccata (MBB; He=0.848, I=2.350, Ne=8.652), M. toringoides (MTH; He=0.663, I=1.355, Ne=3.332), and M. hupehensis (MHR; He=0.539, I=0.912, Ne=0.579) showed a higher level of genetic diversity in this study than the previous studies. MSR and MBB contributed to the origin and evolution of some accessions of M. domestica subsp. chinensis (MDC). However, other accessions of MDC showed a closer genetic distance with MBB and cultivated species, especially M. robusta (MRB), M. asiatica (MAN), and M. prunifolia (MPB). Not all accessions of MDC were descended from MSR in Xinjiang Uygur Autonomous Region of China. This research provides novel insights into the genetic relationships of Malus native to China, which will be useful for genetic association studies, germplasm conservation, and breeding programs.
|
|
Received: 07 July 2020
Accepted:
|
| Fund: This study was funded by the Agricultural Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences (CAAS-ASTIP). |
|
Corresponding Authors:
Correspondence WANG Kun, Mobile: +86-13998907719, Tel/Fax: +86-429-3598120, E-mail: wangkun5488@163.com; CONG Pei-hua, E-mail: congph@163.com
|
| About author: GAO Yuan, E-mail: gaoyuan02@caas.cn; |
Cite this article:
GAO Yuan, WANG Da-jiang, WANG Kun, CONG Pei-hua, LI Lian-wen, PIAO Ji-cheng.
2021.
Analysis of genetic diversity and structure across a wide range of germplasm reveals genetic relationships among seventeen species of Malus Mill. native to China . Journal of Integrative Agriculture, 20(12): 3186-3198.
|
Asuka Y, Tomaru N, Nisimura N, Yamamoto S. 2004. Heterogeneous genetic structure in a Fagus crenata population in an old-growth beech forest revealed by microsatellite markers. Molecular Ecology, 13, 1241–1250.
Baraket G, Chatti K, Saddoud O, Abdelkarim A B, Mars M, Trifi M, Hannachi A S. 2011. Comparative assessment of SSR and AFLP markers for evaluation of genetic diversity and conservation of fig, Ficus carica L., genetic resources in Tunisia. Plant Molecular Biology Reporter, 29, 171–184.
Bellusci F, Palermo A M, Pellegrino G, Musacchio A. 2008. Genetic diversity and spatial structure in the rare, endemic orophyte Campanula pseudostenocodon Lac. (Apennines, Italy), as inferred from nuclear and plastid variation. Plant Biosystems, 1, 24–29.
Byrne M, Macdonald B. 2000. Phylogeography and conservation of three oil mallee taxa, Eucalyptus kochii ssp. kochii, ssp.plenissima and E. horistes. Australian Journal of Botany, 3, 305–312.
Campoy J A, Ruiz D, Egea J, Rees D J G, Celton J M, Martínez-Gómez P. 2011. Inheritance of flowering time in apricot (Prunus armeniaca L.) and analysis of linked quantitative trait loci (QTLs) using simple sequence repeat (SSR) markers. Plant Molecular Biology Reporter, 29, 404–410.
Cao K, Zheng Z J, Wang L R, Liu X, Zhu G R, Fang W C. 2014. Comparative population genomics reveals the domestication history of the peach, Prunus persica, and human influences on perennial fruit crops. Genome Biology, 15, 415.
Cao Y, Tian L M, Gao Y, Yuan J, Zhang S. 2011. Evaluation of genetic identity and variation in cultivars of Pyrus pyrifolia (Burm.f.) Nakai from China using microsatellite markers. Journal of Horticultural Science & Biotechnology, 4, 331–336.
Chen G Q, Huang H W, Ge X J. 2005. Allozyme diversity and population differentiation in an endangered plant, Ammopiptanthus nanus (Leguminosae). Journal of Wuhan Botanical Research, 2, 131–137. (in Chinese)
Chen J, Wang X R, Tang H R, Chen T, Huang X J, Liang Q B. 2013. Assessment of genetic diversity and populations genetic structure in wild Chinese cherry from Sichuan province using SSR markers. Acta Horticulturae Sinica, 2, 333–340. (in Chinese)
Chen X. 2009. A Study on Variation Patterns and Genetic Diversity of Malus hupehensis Populations. Nanjing Forestry University, Nanjing. (in Chinese)
Chen X, Tang G G, Zheng Y H, Wang L H. 2008. RAPD analysis of genetic diversity of Malus baccata (L.) Borkh. Acta Botanica Boreali-Occidentalia Sinica, 10, 1954–1959. (in Chinese)
Cheng M H, Shi S Y, Zhou Z Q. 2004. Studies on the flora of the genus Malus Mill. in Hengduan mountainous region. Scientia Agricultura Sinica, 11, 1666–1671. (in Chinese)
Coart E, Glabeke S, Loose M, Larsen A S, Roldan-Ruiz I. 2006. Chloroplast diversity in the genus Malus: New insights into the relationship between the European wild apple (Malus sylvestris (L.) Mill.) and the domesticated apple (Malus domestica Borkh). Molecular Ecology, 15, 2171–2182.
Dong Y C, Liu X. 2006. Crops and Their Wild Relatives in China. China Agriculture Press, Beijing. (in Chinese)
Duan N B, Bai Y, Sun H H, Wang N, Ma Y M, Li M J. 2017. Genome re-sequencing reveals the history of apple and supports a two-stage for fruit enlargement. Nature Communication, 8, 249.
Earl D A. 2012. STRUCTURE HARVESTER: A website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources, 4, 359–361.
Evanno G, Regnaut S, Goudet J. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study. Molecular Ecology, 14, 2611–2620.
Excoffier L, Lischer H E. 2010. Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources, 10, 564–567.
Fan L, Zhang M, Liu Q, Li L, Song Y, Wang L, Zhang S, Wu J. 2013. Transferability of newly developed pear SSR markers to other Rosaceae species. Plant Molecular Biology Reporter, 31, 1271–1282.
Fan W G, Kang X Y, Fan E P. 1990. The investigation of Malus resources in Guizhou. Journal of Guizhou Academy of Agricultural Science, 1, 93–98. (in Chinese)
Fan W G, Zhu W F, Fan E P. 2002. Germplasm resources of wild fruit tree in Guizhou Province. Journal of Guizhou University, 1, 32–38. (in Chinese)
Forte A V, Ignatov A N, Ponomarenko V V, Dorokhov D B, Savel’ev N I. 2002. Phylogeny of the Malus (apple tree) species inferred from its morphological traits and molecular DNA analysis. Genetika, 10, 1357–1369.
Gardiner S E, Norelli J L, de Silva N, Fazio G, Peil A, Malnoy M. 2012. Putative resistance gene markers associated with quantitative trait loci for fire blight resistance in Malus ‘Robusta 5’ accessions. BMC Genetics, 13, 25.
Geng D L, Lu L Y, Yan M J, Shen X X, Jiang L J, Li H Y, Wang L P, Yan Y, Xu J D, Li C Y, Yu J T, Ma F W, Guan Q M. 2019. Physiological and transcriptomic analyses of roots from Malus sieversii under drought stress. Journal of Integrative Agriculture, 18, 1280–1294.
Gharghani A, Zamani Z, Talaie A, Oraguzie N C, Fatahi R, Hajnajari H. 2009. Genetic identity and relationships of Iranian apple (Malus×domestica Borkh.) cultivars and landraces, wild Malus species and representative old apple cultivars based on simple sequence repeat (SSR) marker analysis. Genetic Resources and Crop Evolution, 6, 829–842.
Godoy J A, Jordan P. 2001. Seed dispersal by animals: Exact identification of source trees with endocarp DNA microsatellites. Molecular Ecology, 10, 2275–2283.
Gu X Z, Cao Y C, Zhang Z H, Zhang B X, Zhao H, Zhang X M, Wang H P, Li X X, Wang L H. 2019. Genetic diversity and population structure analysis of Capsicum germplasm accessions. Journal of Integrative Agriculture, 18, 1312–1320.
Guilford P, Prakash S, Zhu J M, Rikkerink E, Gardiner S, Bassett H. 1997. Microsatellites in Malus×domestica (apple): Abundance, polymorphism and cultivar identification. Theoretical and Applied Genetics, 94, 249–254.
Harris S A, Robinson J P, Juniper B E. 2002. Genetic clues to the origin of the apple. Trends in Genetics, 8, 426–430.
Hokanson S C, Szewc-Mcfadden A K, Lamboy W F, Mcferson J R. 1998. Microsatellite (SSR) markers reveal genetic identities, genetic diversity and relationships in a Malus×domestica borkh. core subset collection. Theoretical and Applied Genetics, 97, 671–683.
Jakobsson M, Rosenberg N A. 2007. CLUMPP: A cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics, 23, 1801–1806.
Jing Q, Liu Y Q, Xie X L. 1996. Investigation and study on wild resources of apple plants in Aba prefecture. Sichuan Fruit Tree, 1, 5–10. (in Chinese)
Juniper B E, Watkins R, Harris S A. 1998. The origins of apple. Acta Horticulturae, 484, 27–33.
Kang H S, Li X D. 1984. The apple resources survey report of Yanyuan County. Sichuan Fruit Tree Technology, 1, 24–25, 27. (in Chinese)
Langenfeld V T. 1991. Apple Trees: Morphological Evolution, Phylogeny, Geography and Systematic of the Genus. Zinatne Publishing, Riga. p. 232.
Letunic I, Bork P. 2016. Interactive tree of life (iTOL) v3: An online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Research, 44, W242–W245.
Li Y N. 2001. Researches of Germplasm Resources of Malus Mill. China Agriculture Press, Beijing. (in Chinese)
Liebhard R, Gianfranceschi L, Koller B, Ryder C D, Tarchini R, Van De Weg E. 2002. Development and characterization of 140 new microsatellites in apple (Malus×domestica Borkh.). Molecular Breeding, 10, 217–241.
Liu J, Zheng X Y, Potter D, Hu C Y, Teng Y W. 2012. Genetic diversity and population structure of Pyrus Calleryana (Rosaceae) in Zhejiang Province, China. Biochemical Systematics and Ecology, 45, 69–78.
Luby J. 2003. Taxonomic classification and brief history. In: Ferree D C, Warrington I J, eds., Apples: Botany Production and Use. CABI Publishing, Cambridge M A.
Luby J, Forsline P, Aldwinckle H, Bus V, Geibel M. 2001. Silk-Road apples - Collection, evaluation and utilization of Malus sieversii from Central Asia. HortScience, 36, 225–231.
Markussen T, Kruger J, Schmidt H, Dunemann F. 1995. Identification of PCR-based markers linked to the powdery-mildew-resistance gene Pl1 from Malus robusta in cultivated apple. Plant Breeding, 6, 530–534.
Nei M, Tajima F, Tateno Y. 1983. Accuracy of estimated phylogenetic trees from molecular data. II. Gene frequency data. Journal of Molecular Evolution, 19, 153–170.
Pan L Q, Ji H, Chen L Q. 2005. Genetic diversity of the natural populations of Adiantum reniforme var. sinense. Biodiversity Science, 2, 122–129. (in Chinese)
Peakall R, Smouse P E. 2012. GenAIEx 6.5: Genetic analysis in Excel. Population genetic software for teaching and research - An update. Bioinformatics, 28, 2537–2539.
Ponomarenko V. 1987. History of Malus domestica borkh origin and evolution. Trudy po prikladnoi botanike, genetike i selektsii, 176, 10–18. (in Russian)
Pritchard J K, Stephens M, Donnelly P. 2000. Inference of population structure using multilocus genotype data. Genetics, 155, 945–959.
Richards C M, Volk G M, Reilley A A, Henk A D, Lockwood D R, Reeves P A. 2009. Genetic diversity and population structure in Malus sieversii, a wild progenitor species of domesticated apple. Tree Genet Genomes, 5, 339–347.
Rosenberg N A. 2004. DISTRUCT: A program for the graphical display of population structure. Molecular Ecology Notes, 4, 137–138.
Shan A, Li D, Gao L M, Li H T, Moller M. 2008. Genetic diversity within and among populations of the endangered species Taxus fauna (Taxaceae) from Pakistan and implications for its conservation. Biochemical Systematics and Ecology, 3, 183–193.
Shi S Y. 2005. Studies on the origin and differentiation of genetic diversity in Malus toringoides. Ph D, Southwest University, Chongqing. (in Chinese)
USDA-ARS (U.S. Department of Agriculture’s Agriculture Research Service). 2015. National genetic resources program. Gerplasm Resources Information Network- (GRIN). National Germplasm Resources Laboratory, Beltsville. [2015-2-12]. http://www.ars-grin.gov.4/cgi-bin/npgs/html/genform.pl
Vavilov N I. 1930. Wild progenitors of the fruit trees of Turkistan and the Caucasus and the problem of the origin of fruit trees. In: Proceedings of the IXth International Horticultural Congress. London. pp. 271–286.
Velasco R, Zharkikh A, Affourtit J. 2010. The genome of the domesticated apple (Malus×domestica Borkh.). Nature Genetics, 42, 833–839.
Vercken E, Fontaine M C, Gladieux P, Hood M E, Jonot O, Giraud T. 2010. Glacial refugia in pathogens: European genetic structure of anther smut pathogens on Silene latifolia and Silene dioica. PLoS Pathogens, 6, e1001229.
Vogt I, Wöhner T, Richter K, Flachowsky H, Sundin G W, Wensing A. 2013. Gene-for-gene relationship in the host–pathogen system Malus×robusta 5–Erwinia amylovora. New Phytologist, 197, 1262–1275.
Volk G M, Henk A D, Baldo A, Fazio G, Chao C T, Richards C M. 2015. Chloroplast heterogeneity and historical admixture within the genus Malus. American Journal of Botany, 7, 198–208.
Wang D J, Wang k, Gao Y, Zhao J R, Liu L J, Gong X. 2017. Preliminary investigation of modern distribution of Malus resources in China. Journal of Plant Genetic Resources, 6, 1116–1124. (in Chinese)
Wang K, Liu F Z, Gao Y, Wang D J, Gong X, Liu L J. 2013. The natural distribution, diversity, and utilization of wild apple species in China. Journal of Plant Genetic Resources, 6, 1013–1019. (in Chinese)
Wang L H, Zheng Y H, Tang G G. 2012. Analyses of genetic diversity and genetic relationship of eight populations of Malus baccata based on SSR marker. Journal of Plant Resources and Environment, 1, 42–46. (in Chinese)
Wright S. 1978. Evolution and the Genetics of Populations, Variability Wthin and Among Natural Populations. The University of Chicago Press, Chicago. p. 4.
Yamamoto T, Kimura T, Shoda M, Ban Y, Hayashi T, Matsuta N. 2002. Development of microsatellite markers in the Japanese pear (Pyrus pyrifolia Nakai). Molecular Ecology Notes, 2, 14–16.
Yan G R, Xu Z. 2010. Study on the Wild Fruit Trees in Xinjiang, China. China Forestry Press, Beijing. (in Chinese)
Zhang C Y, Chen X S, He T M, Liu X L, Feng T, Yuan Z H. 2007. Genetic structure of Malus sieversii population from Xinjiang, China, revealed by SSR markers. Journal of Genetics and Genomics, 10, 947–955.
Zhang D P, Zhang D P, Carbajulca D, Ojeda L, Rossel G, Milla S, Herrera C. 2004. Microsatellite analysis of genetic diversity in sweet potato varieties from Latin America. Genetic Resources and Crop Evolution, 2, 115–120.
Zhang H S, Yan X Q, Lu M, Wang D P, An H M. 2017. Analysis of the genetic diversity of wild Rosa roxburghii populations in Guizhou Province based on EST-SSR marker. Scientia Agricultura Sinica, 6, 1098–1108. (in Chinese)
Zhang X Z, Wang Y, Han Z H. 2010. Analysis on present research and utilization status of wild apple germplasm resources (Malus Mill.) in China. Journal of Agricultural Science and Technology, 3, 8–15. (in Chinese)
Zheng H Z, Li J, Wang S C. 2004. Records of Fruit Germplasm Resources in Tibet. China Agriculture Press, Beijing. (in Chinese) |
| No Suggested Reading articles found! |
|
|
Viewed |
|
|
|
Full text
|
|
|
|
|
Abstract
|
|
|
|
|
Cited |
|
|
|
|
| |
Shared |
|
|
|
|
| |
Discussed |
|
|
|
|
