苹果属植物S-RNase基因型鉴定及起源演化分析

doi:10.1016/j.jia.2024.01.014

摘要/Abstract

摘要： 鉴定苹果属植物S基因型对于新基因的发掘、苹果的栽培生产、新品种选育以及自交不亲和的起源演化等都具有极大的推动作用。本试验以矮花红、西蜀海棠、热磙子等88份苹果属资源为材料，利用7对苹果属S-RNase基因特异性引物，以叶片DNA为模板进行PCR扩增。结果表明：鉴定的供试材料中，70份材料得到完整的S-RNase基因型，18份材料仅鉴定出1个S-RNase基因。经同源性比较分析，共获得13种S-RNase基因型，分别为：S₁S₂(矮花红等)、S₁S₂₈(隰县海棠等)、S₁S₅₁(河北平顶海棠)、S₁S₃(向阳村大果等)、S₂S₃(窄叶海棠等)、S₃S₅₁(西山1号)、S₃S₂₈(黄色立哈尔德等)、S₂S₂₈(红海棠等)、S₄S₂₈(波11)、S₇S₂₈(酒泉沙果)、S₁₀S_e(东城贯13号)、S₁₀S₂₁(东香蕉)、S_eS₅₁(熊岳海棠)。供试材料中S基因出现频率显示：不同的S基因在苹果属资源中出现的频率不同，在种间及种内出现的频率亦不相同。其中出现频率最高的为S₃(68.18%)，其次为S₁(42.04%)。此外，系统进化树及起源演化分析表明，S基因的分化在苹果属各个种形成之前就已完成，栽培种亦演化出了新的S基因，并且分析认为S₅₀基因是苹果属植物最古老的S等位基因，苹果栽培种中的S₁、S₂₉、S₃₃基因可能最初分别起源于新疆野苹果、湖北海棠及陇东海棠。除新疆野苹果外，陇东海棠和锡金海棠可能也参与了部分中国苹果的起源演化过程。

Abstract:

Identification of the S genotype of Malus plants will greatly promote the discovery of new genes, the cultivation and production of apple, the breeding of new varieties, and the origin and evolution of self-incompatibility in Malus plants. In this experiment, 88 Malus germplasm resources, such as Aihuahong, Xishuhaitang, and Reguanzi, were used as materials. Seven gene-specific primer combinations were used in the genotype identification. PCR amplification using leaf DNA produced a single S-RNase gene fragment in all materials. The results revealed that 70 of the identified materials obtained a complete S-RNase genotype, while only one S-RNase gene was found in 18 of them. Through homology comparison and analysis, 13 S-RNase genotypes were obtained: S₁S₂ (Aihuahong, etc.), S₁S₂₈(Xixian Haitang, etc.), S₁S₅₁ (Hebei Pingdinghaitang), S₁S₃ (Xiangyangcun Daguo, etc.), S₂S₃ (Zhaiyehaitang, etc.), S₃S₅₁ (Xishan 1), S₃S₂₈ (Huangselihaerde, etc.), S₂S₂₈ (Honghaitang, etc.), S₄S₂₈ (Bo 11), S₇S₂₈ (Jiuquan Shaguo), S₁₀S_e (Dongchengguan 13), S₁₀S₂₁ (Dongxiangjiao) and S_eS₅₁ (Xiongyue Haitang). Simultaneously, the frequency of the S gene in the tested materials was analyzed. The findings revealed that different S genes had varying frequencies in Malus resources, as well as varying frequencies between intraspecific and interspecific. S₃ had the highest frequency of 68.18%, followed by S₁ (42.04%). In addition, the phylogenetic tree and origin evolution analysis revealed that the S gene differentiation was completed prior to the formation of various apple species, that cultivated species also evolved new S genes, and that the S₅₀ gene is the oldest S allele in Malus plants. The S₁, S₂₉, and S₃₃ genes in apple-cultivated species, on the other hand, may have originated in M. sieversii, M. hupehensis, and M. kansuensis, respectively. In addition to M. sieversii, M. kansuensis and M. sikkimensis may have also played a role in the origin and evolution of some Chinese apples.

Key words: Malus , S-RNase genotype , self-incompatibility , origin and evolution

. 苹果属植物S-RNase基因型鉴定及起源演化分析[J]. Journal of Integrative Agriculture, 2024, 23(4): 1205-1221.

Zhao Liu, Yuan Gao, Kun Wang, Jianrong Feng, Simiao Sun, Xiang Lu, Lin Wang, Wen Tian, Guangyi Wang, Zichen Li, Qingshan Li, Lianwen Li, Dajiang Wang.

Identification of S-RNase genotype and analysis of its origin and evolutionary patterns in Malus plants [J]. Journal of Integrative Agriculture, 2024, 23(4): 1205-1221.

参考文献

Boskovic R, Tobuut K R. 1999. Correlation of stylar ribonuclease isoenzymes with incompatibility alleles in apple. Euphytica, 107, 29–43.

Broothaerts W, Janssens G A, Proost P. 1995. cDNA cloning and molecular analysis of two self-incompatibility alleles from apple. Plant Molecular Biology, 27, 499–511.

Chen H, Zhang S J, Zhang Y Y, Heng W, Zhang S L. 2013. Identification of S-genotypes in forty pear cultivars and analysis of S-RNase genes frequency in Pyrus. Journal of Nanjing Agricultural University, 36, 21–26. (in Chinese)

Ding T Y, Wu M M, Zhang R P, Yan Z L, Yan Y R, Chen D X, Zhang H T, Gao Q M. 2018. Identification of S-genotypes of 20 apple cultivars. Acta Horticulturae Sinica, 45, 2277–2290. (in Chinese)

Duan N B. 2017. Genomic analyses provide new insights into apple evolution, domestication and genetic diversity. Ph D thesis, Shandong Agricultural University, Tai’an, China. (in Chinese)

de Franceschi, Dondini L, Sanzol J. 2012. Molecular bases and evolutionary dynamics of self-incompatibility in the Pyrinae (Rosaceae). Journal of Experimental Botany, 63, 4015–4032.

de Nettancourt D. 1977. Incompatibility in Angiosperms. Springer-Verlag, New York.

East E M, Mangelsdorf A J. 1925. A new interpretation of the hereditary behavior of self-sterile plants. Proceedings of the National Academy of Sciences of the United States of America, 11, 166–171.

Gao Y, Wang D J, Wang K, Cong P H, Li L W, Piao J C. 2020a. Analysis of genetic diversity of apple germplasms of Malus using SLAF-seq technology. Acta Horticulturae Sinica, 47, 1869–1882. (in Chinese)

Gao Y, Wang D J, Wang K, Cong P H, Li L W, Piao J C. 2020b. Genetic diversity and population structure of 17 species of Malus Mill. native to China based on fluorescent SSR analysis. Journal of Fruit Science, 37, 1611–1622. (in Chinese)

Gao Y, Wang D J, Wang K, Cong P H, Li L W, Piao J C. 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, 3186–3198.

He M, Gu C, Wu J Y, Zhang S L. 2021. Recent advances on self-incompatibility mechanism in fruit trees. Acta Horticulturae Sinica, 48, 759–777. (in Chinese)

He M, Li L F, Xu Y, Mu J X, Xie Z H, Gu C, Zhang S L. 2022. Identifification of S-genotypes and a novel S-RNase in 84 native Chinese pear accessions. Horticultural Plant Journal, 8, 713–726.

Hoy T K, Gen H, Yutaka H, Dae I K, Jeong H H, Yong U S, Ill S N. 2006. Determination of self-incompatibility genotypes of Korean apple cultivars based on S-RNase PCR. Journal of Plant Biology, 49, 448–454.

Hu G F, Ni Z J, Daouda C, Gao Z H. 2021. Identification of S genotype and novel S-RNase genes in Japanese apricot (Prunus mume Sieb. et Zucc.). Journal of Plant Genetic Resources, 22, 860–872. (in Chinese)

Jiang N, Zhang L, Tan X F, Tan H, Zhang J G. 2017. Detection of S-genotypes and evolution analysis of novel S-RNase genes identified by cDNA microarray-based method. Journal of Plant Genetic Resources, 18, 520–529. (in Chinese)

Kao T H, Tsukamoto T. 2004. The molecular and genetic bases of S-RNase-based self-incompatibility. The Plant Cell, 16, 72–83.

Kim H, Park J, Hirata Y, Nou I. 2008. Molecular characterization of new S-RNases (‘S₃₁’ and ‘S₃₂’) in apple (Malus domestica Borkh.). Journal of Plant Biology, 3, 202–208.

Kobel F, Steinegger P, Anliker J. 1939. Further study on pollination mechanism of apple. Landw Jb Schweiz, 53, 160–191. (in German)

Li H L, Zhang B B, Liang Y H, Zhao C H, Wang S S, Song H W. 2020. Analysis of apple breeding parents selection and crosses in recent 30 years of China. Molecular Plant Breeding, 18, 7155–7161. (in Chinese)

Li T Z, Long S S, Li M F, Bai S L, Meng D. 2011. Advances in research of the self-incompatibility genotypes (S-genotypes) in apple. Scientia Agricultura Sinica, 44, 1173–1183. (in Chinese)

Li Y, Liu C S, Yu J, Song B X W, Wang K, Liu Z, Li T Z. 2017. The establishment of apple S genotype database and instruction. China Fruits, 5, 5–8. (in Chinese)

Li Y N. 1999. Progress in research on the origin and evolution of genus Malus in the world. Journal of Fruit Science, (S1), 8–19. (in Chinese)

Li Y N. 2001. Study on the Germplasm Resources of Malus. China Agriculture Press, China. (in Chinese)

Liang M. 2019. Gene identification and evolution of self-incompatibility of Citrus. Ph D thesis, Huazhong Agricultural University, China. (in Chinese)

Long S S, Li M F, Han Z H, Wang K, Li T Z. 2010a. Characterization of three new S-alleles and development of an S-allele-specific PCR system for rapidly identifying the S-genotype in apple cultivars. Tree Genetics and Genomes, 6, 161–168.

Long S S, Li M F, Han Z H, Zhang B B, Wang K, Li T Z. 2010b. Characterization of two novel S-RNase genes and PCR analyzing of S-genotypes of 46 cultivars in Malus domestica Borkh. Journal of Agricultural Biotechnology, 18, 265–271. (in Chinese)

Lv A M. 2015. Calculation and influencing factors of gene frequency and genotype frequency. Biology Teaching, 40, 37–39. (in Chinese)

Matsumoto S, Furusawa Y, Kitahara K, Soejima J. 2003. Partial genomic sequences of S₆_-, S₁₂_-, S₁₃_-, S₁₄_-, S₁₇_-, S₁₉_-, and S₂₁_-RNaseof apple and their allele designations. Plant Biotechnology, 20, 323–329.

McClure B. 2006. New views of S-RNase-based self-incompatibility. Current Opinion Plant Biology, 9, 639–646.

Sassa H. 2016. Molecular mechanism of the S-RNase based gametophytic self-incompatibility in fruit trees of Rosaceae. Breeding Science, 66, 116–121.

Sassa H, Mase N, Hirano H. 1994. Identification of self-incompatibility related glycoproteins in styles of apple (Malus×domestica). Theoretical and Applied Genetics, 89, 201.

Stein J C, Howlerr B, Boyes D C, Nasrallah M E, Nasrallah J B. 1991. Molecular cloning of a putative receptor protein kinase gene encoded at the self-incompatibility locus of Brassica oleracea. Proceedings of the National Academy of Sciences of the United States of America, 88, 8816–8820.

Sun X P, Jiao C, Schwaninger H D, Chao T, Ma Y M, Duan N B, Khan A, Ban S H, Xu K N, Cheng L L, Zhong G Y, Fei Z J. 2020. Phased diploid genome assemblies and pan-genomes provide insights into the genetic history of apple domestication. Nature Genetics, 52, 1423–1432.

Takayama S, Isogai A. 2005. Self-incompatibility in plants. Annual Review of Plant Biology, 56, 467–489.

Takayama S, Shiba H, Iwano M, Shimosato H, Che F S, Kai N, Watanabe M, Suzuki G, Hinata K, Isogai A. 2000. The pollen determinant of self-incompatibility in Brassica campestris. Proceedings of the National Academy of Sciences of the United States of America, 97, 1920–1925.

Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, Kalyanaraman A, Fontana P, Bhatnagar S K, Troggio M, Pruss D, Salvi S, Pindo M, Baldi P, Castelletti S, Cavaiuolo M, Coppola G, Costa F, Cova V, Ri A D, Goremykin V, et al. 2010. The genome of the domesticated apple (Malus domestica Borkh.). Nature Genetics, 42, 833–839.

Verdoodt L, Van H A, Goderis I J, De W K, Keulemans J, Broothaerts W. 1998. Use of the multi-allelic self-incompatibility gene in apple to assess homozygosity in shoots obtained through haploid induction. Theoretical and Applied Genetics, 96, 294–300.

Wei Z M, Wei S J, Chen P, Hu J B, Tang Y Q, Ye J L, Li X X, Deng X X, Chai L J. 2022. Identification of S-genotypes of 63 Pummelo germplasm resources. Acta Horticulturae Sinica, 49, 1111–1120. (in Chinese)

William A H. 1982. Chemical evidence from the flavonoide relevent of the classification of Malus species. Botanical Journal of the Linnean Society, 84, 31–39.

Xu G H, Zhang S L, Yang Y H, Zhao C P, Wolukau J N. 2008. Influence of endogenous and exogenous RNases on the variation of pollen cytosolic-free Ca²⁺ in Pyrus serotina Rehd. Acta Physiologiae Plantarum, 30, 233–241.

Yu D J. 1984. Origin and evolution of Rosaceae. Acta Phytotaxonomica Sinica, 22, 431–444. (in Chinese)

Zeng B, Gao Q M, Tian J, Li J. 2014. Analysis and identification of self-incompatibility S-RNase genotype of almond varieties in Xinjiang. Xinjiang Agricultural Sciences, 51, 1400–1408. (in Chinese)

Zhang M M, Wang Z H, Mao Y F, Chai S S, Zhao X H, Fan Y C, Ni W, Mao Z Q, Chen X S, Shen X. 2018. Effects of different pollination combinations on the fruit quality of ‘Fuji’ and ‘Starkrimson’ apple. Scientia Agricultura Sinica, 51, 3551–3560. (in Chinese)

Zhang X M, Li B G, Qi G H, Guo S P. 2013. Isolation and identification of self-incompatibility allele in 11 apple cultivars. Journal of Plant Genetic Resources, 14, 311–321. (in Chinese)

Zhang Y Y, Wu J, Heng W, Zhang S L. 2006. Identification of S-genotypes of pear cultivars and analyses of nucleotide sequences of S₂₈-RNase and S₃₀-RNase. Acta Horticulturae Sinica, 33, 496–500. (in Chinese)

Zhao J L, Zhang Y S. 2019. Study on pollination effects of 8 pollination cultivars on ‘Qiufu 1’ apple. China Fruits, (1), 46–49. (in Chinese)