基于核基因序列JRD5680的核桃群体遗传多样性和遗传结构研究

doi:10.7525/j.issn.1673-5102.2016.02.012

摘要/Abstract

摘要： 以40个核桃（Juglans regia）地理群体及5个外类群植物为材料，利用苯丙氨酸解氨酶基因片段JRD5680序列对265个个体研究了我国不同地区核桃的群体遗传多样性、群体遗传结构以及单倍型地理分布。结果表明：核基因JRD5680序列长度为809 bp，其中G+C碱基含量为46.2%，74个简约性信息位点。共30个单倍型，单倍型多样性变异小，表现出较低的遗传多样性（H_d=0.370，π=0.005 3）。核桃群体间有明显的谱系地理学结构（N_ST>G_ST），呈现地域性分布格局的特点。空间遗传结构分析表明，地理隔离距离与遗传距离之间也显示两者之间相关性显著（r=0.263 2；P=0.032 4*），不同地理分布核桃群体间存在着明显地理隔离效应。综合失配分析及中性检验的结果，可推断出近期历史上不同地区核桃没有发生群体扩张事件。遗传结构显示，核桃群体可分为两组（西南地区与其他地区）。AMOVA分析结果表明，核桃群体遗传变异主要存于群体之间（56.54%），不同种之间的遗传分化水平较高（F_ST=0.885）。单倍型系统发育树中核桃与外类群物种均能形成单系分支，说明JRD5680序列在胡桃科中的具有较高的分子鉴别率。

关键词: 核桃, 苯丙氨酸解氨酶基因, 遗传多样性, 遗传结构

Abstract: We studied the genetic diversity and population genetic structure of 265 individuals from different regions of China by using the roles of phenylalanine ammonia-lyase(PAL) nuclear gene JRD5680 DNA sequence of 40 common walnut(Juglans regia) and 5 out group plant species. The length of JRD5680 sequence was 809 bp, the content of G+C was 46.2% with 74 information sites. A total of 30 haplotypes, haplotype diversity variation showed low genetic diversity(H_d=0.370, π=0.005 3). There is a clear geographical structure(N_ST>G_ST), which is a regional distribution pattern. The spatial genetic structure analysis showed that the correlation between geographical isolation and genetic distance was significant(r=0.263 2; P=0.032 4*), and there was obvious geographical isolation effect among different geographic populations. The results of comprehensive mismatch analysis and neutral test can be deduced from the recent history of the different regions of the population expansion event. From the genetic structure, the walnut population can be divided into two groups(southwest and other regions). By AMOVA, the genetic variation among the populations was mainly stored in the populations(56.54%), and the genetic differentiation among the populations was higher(F_ST=0.885). The total of 5 species of Juglandaceae could be a single branch, and the JRD5680 sequence might be with high molecular identification radio in the members of the Juglandaceae.

Key words: Juglans regia, phenylalanine ammonia-lyase(PAL) gene, genetic diversity, genetic structure

张甜；王玛丽；赵鹏*. 基于核基因序列JRD5680的核桃群体遗传多样性和遗传结构研究[J]. 植物研究, 2016, 36(2): 232-241.

ZHANG Tian；WANG Ma-Li；ZHAO Peng*. Sequence Analysis of Nuclear DNA JRD5680 for Determining Genetic Diversity and Genetic Structure Analysis of Common Walnut(Juglans regia L.)[J]. Bulletin of Botanical Research, 2016, 36(2): 232-241.

参考文献

1.Beer R,Kaiser F,Schmidt K,et al.Vegetation history of the walnut forests in Kyrgyzstan(Central Asia):natural or anthropogenic origin?［J］.Quaternary Sci Rev,2008,27(5):621-632.

2.Hoban S M,Borkowski D S,Brosi S L,et al.Range-wide distribution of genetic diversity in the North American tree Juglans cinerea:a product of range shifts,not ecological marginality or recent population decline［J］.Mol Ecol,2010,19(22):4876-4891.

3.Ishihama F,Ueno S,Tsumura Y,et al.Gene flow and inbreeding depression inferred from fine-scale genetic structure in an endangered heterostylous perennial,Primula sieboldi［J］.Molecular Ecology,2005,14(4):983-990.

4.Epperson B K.Spatial distributions of genotypes under isolation by distance［J］.Genetics,1995,140(4):1431-1440.

5.Escudero A,Iriondo J M,Torres M E.Spatial analysis of genetic diversity as a tool for plant conservation［J］.Biol Conserv,2003,113(3):351-365.

6.Vinson J A,Cai Y.Nuts,especially walnuts,have both antioxidant quantity and efficacy and exhibit significant potential health benefits［J］.Food Funct,2012,3(2):134-140.

7.肖志娟,翟梅枝,王振元,等.微卫星DNA在分析核桃遗传多样性上的应用［J］.中南林业科技大学学报,2014,34(2):55-61.

8.Fjellstrom R G,Parfitt D E.Phylogenetic analysis and evolution of the genus Juglans(Juglandaceae) as determined from nuclear genome RFLPs［J］.Plant Syst Evol,1995,197(1-4):19-32.

9.Zhao P,Woeste K E.DNA markers identify hybrids between butternut(Juglans cinerea L.) and Japanese walnut(Juglans ailantifolia Carr.)［J］.Tree Genet Genomes,2011,7(3):511-533.

10.Dangl G S,Woeste K,Aradhya M K,et al.Characterization of 14 microsatellite markers for genetic analysis and cultivar identification of walnut［J］.J Am Soc Hortic Sci,2005,130(3):348-354.

11.王红霞,张志华,赵书岗,等.核桃种质资源遗传多样性研究中的AFLP技术优化及引物筛选［J］.华北农学报,2008,23(1):50-54.

12.丁铭,曾丽萍,马红,等.初探低拷贝核基因在低等分类阶元系统发育重建中的适用性—以十字花科为例［J］.植物分类与资源学报,2012,34(3):211-221.

13.吴春燕,高立志.六个核基因片段在中国颗粒野生稻中的单核苷酸多态性及其在群体遗传学研究中的应用［J］.植物分类与资源学报,2013,35(5):537-546.

14.Doyle J J.A rapid DNA isolation procedure for small quantities of fresh leaf tissue［J］.Phytochem bull,1987,19(1):11-15.

15.赵鹏,Keith Woeste,程飞,等.美国黑核桃SSR反应体系优化［J］.植物研究,2012,32(2):213-221.

16.Pina A,Errea P.Differential induction of phenylalanine ammonia-lyase gene expression in response to in vitro callus unions of Prunus spp.［J］.J Plant Physiol,2008,165:705-714.

17.Olsen K M,Lea U S,Slimestad R,et al.Differential expression of four Arabidopsis PAL genes;PAL1 and PAL2 have functional specialization in abiotic environmental-triggered flavonoid synthesis［J］.J Plant Physiol,2008,165:1491-1499.

18.Hall T A.BioEdit:a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT［C］.//Nucleic acids symposium series,1999,41:95-98.

19.Librado P,Rozas J.DnaSP v5:a software for comprehensive analysis of DNA polymorphism data［J］.Bioinformatics,2009,25(11):1451-1452.

20.Tajima F.Statistical method for testing the neutral mutation hypothesis by DNA polymorphism［J］.Genetics,1989,123(3):585-595.

21.Fu Y X,Li W H.Statistical tests of neutrality of mutations［J］.Genetics,1993,133(3):693-709.

22.Rogers A R,Harpending H.Population growth makes waves in the distribution of pairwise genetic differences［J］.Mol Biol Evol,1992,9(3):552-569.

23.Bandelt H J,Forster P,Röhl A.Median-joining networks for inferring intraspecific phylogenies［J］.Mol Biol Evol,1999,16(1):37-48.

24.Pritchard J K,Stephens M,Donnelly P.Inference of population structure using multilocus genotype data［J］.Genetics,2000,155(2):945-959.

25.Excoffier L,Laval G,Schneider S.Arlequin(version 3.0):an integrated software package for population genetics data analysis［J］.Evol Bioinform,2005,1:47.

26.Tamura K,Peterson D,Peterson N,et al.MEGA5:molecular evolutionary genetics analysis using maximum likelihood,evolutionary distance,and maximum parsimony methods［J］.Mol Biol Evol,2011,28(10):2731-2739.

27.Jensen J L,Bohonak A J,Kelley S T.Isolation by distance,web service［J］.BMC Genet,2005,6(1):13.

28.李俊清.植物遗传多样性及保护研究进展［J］.植物研究,1998,18(2):226-242.

29.王静,张小平,李文良,等.濒危植物连香树居群的遗传多样性和遗传分化研究［J］.植物研究,2010(2):208-214.

30.Joly C,Visset L.Evolution of vegetation landscapes since the Late Mesolithic on the French West Atlantic coast［J］.Rev Palaeobot Palyno,2009,154(1):124-179.

31.刘方春,邢尚军,马海林,等.干旱生境中接种根际促生细菌对核桃根际土壤生物学特征的影响［J］.应用生态学报,2014,25(5):1475-1482.

32.Akca Y,Samsunlu E.The effect of salt stress on growth,chlorophyll content,proline and nutrient accumulation,and K/Na ratio in walnut［J］.Pak J Bot,2012,44(5):1513-1520.

33.冯连芬,吕芳德,张亚萍,等.我国核桃育种及其栽培技术研究进展［J］.经济林研究,2006,24(2):69-73.

34.Hamrick J L,Godt M J W.Conservation genetics of endemic plant species［M］.Conservation genetics.Springer US,1996:281-304.

35.奚声珂.我国胡桃属(Juglans L.) 种质资源与核桃(Juglans regia L.) 育种［J］.林业科学,1987,23(3):342-349.

36.Aradhya M K,Potter D,Gao F,et al.Molecular phylogeny of Juglans(Juglandaceae):a biogeographic perspective［J］.Tree Genet Genomes,2007,3(4):363-378.

37.赵鹏,周惠娟,刘占林,等.胡桃属植物分子系统发育和生物地理研究进展［J］.林业科学,2014,50(11):147-157.

38.赵大鹏,王康满,侯元同.基于叶绿体trnL-F,rbcL序列和核糖体ITS序列探讨廖属（廖科）头状廖组的系统发育［J］.植物研究,2012,32(1):77-83.

39.胡昳恒,党萌,张甜,等.秦岭地区核桃自然群体和栽培群体的遗传多样性及其演化关系—基于nrDNA ITS序列分析［J］.林业科学,2014,50(12):47-55.

[1]	杨磊, 曹秋梅, 冯缨, 李文军. 珍稀濒危植物阜康阿魏的遗传多样性及遗传结构[J]. 植物研究, 2023, 43(1): 51-58.
[2]	唐思如, 王铁娟, 秀芳, 刘梦瑶, 张慧. 基于单拷贝核基因的褐沙蒿遗传结构和谱系地理学分析[J]. 植物研究, 2022, 42(6): 956-963.
[3]	常二梅, 刘建锋, 黄跃宁, 李红丽, 单冰燕, 江泽平, 赵秀莲. 岷江柏野生居群和迁地保护居群的遗传多样性比较[J]. 植物研究, 2022, 42(5): 772-779.
[4]	张玉洁, 石鹏霞, 赵凡, 陈晓丹, 孙坤, 张辉. rpl32-trnL片段在柳穿鱼不同地理居群遗传多样性分析中的应用[J]. 植物研究, 2022, 42(5): 780-789.
[5]	张阳, 马子兰, 徐珊珊, 苏旭, 李梅英. 青藏高原东北部黄缨菊的谱系地理学[J]. 植物研究, 2022, 42(4): 565-573.
[6]	张宏斌, 吕东, 赵明, 赵祜, 赵兴鹏, 李伟. 基于全基因组SNP分子标记分析青海云杉遗传结构[J]. 植物研究, 2022, 42(3): 373-382.
[7]	马凯恒, 何佳凝, 谢牧洪, 任斌, 黄倩雪, 杨桂燕. 核桃JrNPR1基因的克隆与抗病响应潜力[J]. 植物研究, 2022, 42(1): 39-46.
[8]	张序, 张秀姣, 马永鹏, 李正红, 万友名, 马宏. 基于GBS简化基因组技术的宽杯杜鹃遗传多样性分析[J]. 植物研究, 2021, 41(3): 429-435.
[9]	段义忠, 王海涛, 张格格, 严伟娜. 基于ISSR分子标记的孑遗濒危植物四合木遗传结构分析[J]. 植物研究, 2021, 41(3): 466-473.
[10]	吕冬雪, 张学杰, 张洛艳, 樊守金. 基于SSR技术对黄河三角洲二色补血草遗传多样性研究[J]. 植物研究, 2020, 40(6): 923-931.
[11]	宁馨, 姜小龙, 邓敏, 徐刚标. 基于简化基因组数据开发岭南青冈微卫星引物[J]. 植物研究, 2020, 40(4): 629-634.
[12]	及利, 韩姣, 王芳, 王君, 宋笛, 张丽杰, 祁永会, 杨雨春. 干旱胁迫对不同土壤基质下核桃楸幼苗的生理特性的影响[J]. 植物研究, 2019, 39(5): 722-732.
[13]	管睿婷, 刘济明, 王敏, 陈敬忠, 武梦瑶, 童炳丽. 不同天然居群小蓬竹的遗传多样性[J]. 植物研究, 2019, 39(5): 740-751.
[14]	郭文丽, 李义良, 赵奋成, 铁军, 廖仿炎, 钟岁英, 林昌明, 叶威方. 湿加松无性系表型遗传多样性研究[J]. 植物研究, 2019, 39(2): 259-266.
[15]	刘济明, 管睿婷, 王敏, 陈敬忠, 童炳丽, 武梦瑶. 不同喀斯特小生境中小蓬竹的遗传多样性[J]. 植物研究, 2019, 39(1): 69-77.