Human Genome Diversity Research in China Chu Jiayou, Institute of Medical Biology, Chinese Academy of Medical Sciences, Kunming 650118 There are 56 nationalities in China, each of them having independent inhabitation areas. And some of them are genetic isolated population. In the source of nationalities and genetic phenotypes, each nationality has its unique characteristics. There are significant differences in categories, enzyme system,HLA antigen and incidences of some genetic diseases. Yi Jino Dulong Lisu Bai Achang Naxi Hani Pumi Tibetan Lahu Chinese populations Nationalities Population .Nationalities Population .Nationalities Population ** Achang 27,708 **Jingpo 119,209 Qiang 198,252 **Bai 1,594,827 **Jino 18,000 Russian 13,504 Baoan 12,212 Kazak 1,111,718 Sala 87,697 **Blang 82,280 Kirgiz 141,549 She 630,378 *Bouye 2,545,059 Korean 1,920,597 *Shui 345,993 **Dai 1,025,128 **Lahu 411,476 Tajik 33,583 Daur 121,357 Lhoba 2,312 Tatar 4,873 **De'ang 15,462 Li 1.110,000 *Tibetan 4,593,330 Dong 2,514,014 **Lisu 574,856 Tu 191,624 Dongxiang 373,872 *Manchu 9,821,180 Tujia 5,704,223 **Dulong 5,816 Maonan 71,968 Uygur 7,214,431 Ewenki 26,315 *Miao 7,398,035 Uzbek 14,502 Gaoshan 400,000 Moinba 7,475 **Wa 351,974 Gelao 437,997 *Mongolian 4,806,849 Xibe 172,847 *Han 1.2 billion Mulao 159,328 *Yao 2,134,013 **Hani 1,253,952 **Naxi 278,009 *Yi 6,572,173 Hezhe 4,245 **Nu 21,723 Yugur 10,569 *Hui 8,602,978 Oroqen 6,965 *Zhuang 15,489,630 Jing 18,915 **Pumi 29,657 _____________________________________________________________________________________ * and ** distributed in Yunnan province. ** only resided in Yunnan province Chinese Human Genome Diversity ,As a part of Chinese Human Genome Project Biodiversity is so important, human being should not forget it’s own diversity. ____ Prof. Min Wu, A Chinese Human Genome Project founder of Why human genome diversity research in China is focused in Yunnan province.? Among 56 nationalities of China, there are 26 nationalities with populations of more than 5000 living together in Yunnan province. Among 26 nationalities, 15 are only living in Yunnan province: Bai, Hani, Dai, Lisu, Lahu, Wa, Naxi, Jingpo, Bulang, Pumi, Nu, Achang, Deang, Jino and Dulong. Geographical Distribution of Sino-Tibetan Populations Geographical Distribution of Sino-Tibetan Populations Why are so many nationalities in Yunnan province? 1 . Specific historic reasons make many nationalities migrating to Yunnan. During the 5th century B.C. to 3rd century B.C., Xiongnu people in Mongolian Plain became stronger gradually and began to expand its territory to Qinhai and Gansu province. As a result, two ancient nationalities of Di and Qiang were expelled to the southwest China. In addition, ancient wars made some nationalities migrate to Yunnan to seek asylum. From then on, these nationalities settled down in Yunnan province. 2 . Complicated geography and climate of Yunnan. The complicated geographic environment, climate and rich natural resources in Yunnan province just fit for those different nationalities’ living customs. Therefore, Yunnan becomes an ideal place for many nationalities to settle down. 3 . Yunnan is isolated from outside for a period of time. Yunnan province is isolated from outside because of long-term feudal rule, regional domination and inaccessibility in transportation. Furthermore, separating from outside, backward mode of production and lower needs for living made many nationalities keeping in a independent and isolated state. At present, more and more youths are married each other among different nationalities, genome of some nationalities face the danger of extinction. Therefore, the reservation of different nationalities genome become an urgent project. If measures have not been taken from now on , we will lose the opportunity forever. Three focuses of our study 1. 2. 3. Reservation of different Chinese populations’ genome (cell bank and genome DNA bank). Research on genetic diversity. Research on relationship between diversity and disease gene. Co-operation groups -Institute of Medical Biology, Chinese Academy of Medical Sciences,Kunming -Harbin Medical University,Harbin -Institute of Genetics, Chinese Academy of Sciences, Beijing -Chinese Western Medical College,Chengdu -Fudan University,Shanghai Examples of our Current Work 1 Sample collection and cell line Establishment For this study, consulting with nationality scholars , blood samples of healthy individuals with no relative tie belong to different populations were collected at ethnic groups’ living areas, and 3 generations are investigated and recalled. This can guarantee the representative of samples. More attentions will be paid to collect some samples from special genetic disease cases and cases with special phenotypes. To sample large families with specific characteristics of the ethnic group is also in the plan. Based on the principle of “informed consent” Giving medical consulting service for local people DNA were extracted from blood samples and qualified. Meanwhile, use EB virus transformation technique to establish the genetic specific immortalized lymphocyte lines of different nationalities. 中华民族基因组的保存情况Chinese Different Nationalities’ Gene Bank Ethnic groups Sampling place cell line DNA Samples Sala She Tu Naxi Xunhua County, Qinghai Province Fuan City, Fujian Province Huzhu County, Qinghai Province Lijiang City, Yunnan Province Jinghong City, Xishuangbanna Autonomous Region & Luxi county, Dehong, Dai and Jingpo Autonomous Region, Yunnan Province Luxi County, Dehong, Dai and Jingpo Autonomous Region, Yunnan Province Luxi County, Dehong, Dai and Jingpo Autonomous Region, Yunnan Province Lhasa City, Tibet Autonomous Region Baise County, Guangxi Zhuang Auto nomous Region Luxi County, Dehong, Dai and Jingpo Autonomous Region, Yunnan Province Baisha County, Hainan Province Yongning Xiang, Ninglang County, Yunnan Province Wangqiao Xiang, Dali, Yunnan Province Paomaping Xiang, Ninglang County, Yunnan Province Shaoguan City, Guangdong Province Najiaying Town, Tonghai County, Yunnan Province 71 49 39 36 100 100 100 100 62 100 49 100 55 100 51 100 55 100 45 100 57 100 43 100 61 100 47 100 61 100 50 100 Dai Jingpo De’ang Tibetan Zhuang Bulang Li Moso Bai Yi Han-GD Hui Ethnic groups Han_SD Lisu Nu Dai-Huayao Oroqen Ewenki Daur Mongol Koreans Hezhen Man Xibe Han-Sichuan Han_Fujian Sampling place Zhouping County Shandong Province Fugong County, Nujiang, Yunnan Province Fugong County, Nujiang, Yunnan Province Xinping County, Yunnan Province Ali river Oroqen Autonomous County, Nei Mongol Province Na river County, Heilongjiang Province Hongyan Daur Autonomous county, Nei Mongol Province Haila’er City, Nei Mongol Province Yanbian Koreans Autonomous Region, Jilin Province Tongjiang County, Heilong jiang Province Youyian Man Autonomous county, Liaoling Province Chabu’er Xibe Autonomous County, Xinjiang Province Leyu County, Sichuang Province Minqing County, Fujian Province cell line DNA Samples 61 100 56 100 57 100 5 100 39 120 43 120 58 120 62 120 58 120 18 120 65 120 43 120 51 58 120 120 Ethnic groups Hui Kazak Bouyei Dong Qiang Kirgiz Han-Hunan Han-Shanxi Han-Guangdong Yi Miao Tujia Han-Zhejiang Han-Henan Uygur Yao Total Sampling place cell line DNA Samples 63 120 64 120 67 120 50 48 57 100 100 100 59 100 58 100 Tongxin County, Ningxia Hui Autonomous Region, Xinjiang Province Yinin Kazak Autonomous Region Qiannan Bouyei Autonomous Region, Guizhou Province Sanjiang County, Guangxi Province Mao County, Sichuang Province Wuqia County, Xinjiang Province Shuangfeng County, Hunan Province Linyou County, Shanxi Province Guangning County, Guangdong Province Butuo County, Sichuan Province Songtao County, Guizhou Province Laifeng County, Hubei Province Jinyun County, Zhejiang Province Fangcheng County, Henan Province YIning City, Xinjiang Province 55 100 49 43 56 59 60 60 100 100 100 100 100 100 Du’an County, Guangxi Province 58 100 2411 4860 Examples of our Current Work 2 Research on genetic diversity STR Y Chromosome mtDNA SNP Y Chromosome markers • SNPs (Single Nucleotide Polymorphisms) Mutation rate is low Trace the ancient events • Microsatellites (Tandem repeat of 2-5 nt) Mutation rate is high Trace the recent events Estimate the age of MRCAs Allelic Specific PCR in Multiplex of Five Y Chromosome SNPs M 1 2 3 4 5 6 7 8 M89 ( 365bp ) M110 ( 250bp ) M50 ( 219bp) M7 ( 174bp ) M119 ( 144bp ) Y Chromosome Haplotype Frequency Distributions in East Asian Populations Cont ine nt East Asia Pop ulatio n Buryat (1) Ewenki (2) Manchurian (3) Mongolia n(4) Korean (5) Japanese (6) Hui (7) Tibetan (8) Jingpo (9) Tuji a (10) Yao-Nandan (11) Yao-Jin xiu (12) Z huang(13) Dong (14) Bulang (15) Lahu (16) Yi (17) She (18) Atayal (19) Yami (20) Paiw an (21) Ami (22) Li (23) Cambodia n (24) NE. Thai (25) Malays ia n (26) Batak (27) Javanes e (28) Siz e 4 8 18 24 7 29 20 8 5 10 10 10 29 10 5 5 14 11 24 8 11 6 11 26 20 13 18 11 H1 75 50 17 58 21 10 10 50 20 3.6 20 20 20 H2 H3 H4 25 4.2 11 8.3 28 5 13 20 13 25 30 3.6 7.1 H5 H6 13 22 13 57 21 30 13 28 4.2 20 20 30 3.6 H7 17 10 30 10 3.6 10 H8 25 17 5.6 4.2 4.2 43 10 3.4 20 50 100 20 25 20 10 20 14 43 9.1 21 18 29 27 4.2 7.1 18 4.2 18 5.6 9.1 18 20 3.8 12 5 7.7 5.6 9.1 12 5 7.7 11 27 3.8 5 31 11 9.1 9.1 15 5 15 17 54 25 55 100 27 3.8 5 7.7 22 18 10 5 3.8 5 3.8 10 60 18 3.8 H9 H10 H11 H12 H13 H14 H15 H16 H17 40 25 20 60 20 14 9.1 11 8.3 75 27 3.8 5 23 9.1 55 23 45 7.7 28 18 9.1 12 20 YAP+ YAP+(%) Han Diversity Han(Guandong) Han(Shanxi) Han(North) Han(Yunnan) 0 0 0 0 Northern populations Ewenki Oraqen Daur Man Uygur Hui 0 0 0 0 4 8 YAP+(%) Southern populations Zhuang Lahu Wa Dai Tujia Yao Yi Tibeten(Yunnan) Tibeten(Tibet) 0 0 0 0 2 2 15 39 49 Multiple origins of Tibetan The YAP+ is an ancient polymorphism that originated from Central Asia (Altheide and Hammer, 1997) Our previous study on extant East Asian populations showed that M122C (defining H6, H7 and H8) is predominant in East Asian populations, especially in Han Chinese (54.1% on average) (Su et al., 1999) but it is nearly absent in other world populations, including Central Asians (RS Wells, personal communication). Based on the fact of presentation with high frequency of both YAP +(41.3% in Zang and 44.4% in Khamba) and M122C (>35%), reflects a genetic source of Tibetan Ychromosomes may have been derived from two different gene pools, one from Central Asia and the other from East Asia SNP(Single Nuleotide Polymorphisms) • SNP application – Linkage analysis – Association study – Population genetics – Evolution – Complex disease study – Pharmacogenomics – Individual medical The 126 genes of 21 chromosome were sequenced 1 ABCG1 45 D SCR5 89 PKNOX1 112 T FF3 2 A D A M T S1 24 CBS 68 K CN J15 113 T IA M 1 3 A D A M T S5 25 CCT 8 69 K CN J6 114 T M EM 1 4 A D A RB1 26 CH A F 1B 70 K IA A 0179 115 T M P RSS2 5 A IRE 27 CLD N 14 71 K IA A 0184 116 T PT E 6 APP 28 CLD N 17 72 K IA A 0539 117 T RP C7 7 AT P 50 29 CLD N 8 73 K IA A 0653 118 T SG A 2 8 AT P 5A 30 CO L18A 1 74 K IA A 0958 119 T T C3 9 B3G A LT 5 31 CO L6A 1 75 K IA A O 136 120 U 2A F 1 10 BA CE2 32 CO L6A 2 76 LSS 121 U BE2G 2 11 BA CH 1 33 CRYA A 77 M CM 3 122 U SP 16 12 BT G 3 34 CRYZ L1 78 M X1 123 U SP 25 13 C21orf1 35 CST B 79 M X2 124 WD R4 14 C21orf18 36 CT BP 2 80 N 143 125 WD R9 15 C21orf2 37 CX A D R 81 N CA M 2 126 WRB 16 C21orf258 38 D 21S2056E 82 N D U F V3 17 C21orf30 39 D N M T 3L 83 N RIP 1 18 C21orf33 40 D SCA M 84 P CN T 19 C21orf4 41 D SCR1 85 P CP 4 20 c21orf5 42 D SCR2 86 P D E9A 21 C21orf6 43 D SCR3 87 PDXK 22 CBR1 44 D SCR4 88 PFKL 23 CBR3 67 K CN E2 111 T FF2 The individual samples No1. A01 A02 A03 A04 A05 A06 A07 A08 A09 A10 A11 A12 B01 B02 B03 B04 B05 B06 B07 B08 B09 B10 B11 B12 C01 C02 C03 C04 C05 C06 C07 C08 property individual individual individual individual individual individual individual individual individual control(-) individual individual individual individual individual individual individual individual individual individual individual individual individual individual individual individual individual individual individual individual individual individual No2. I1 I2 I3 I4 I5 I6 I7 I8 I9 Sample Sun L Han F Liu H Zhu L BF28 BF29 Meng S Huang g Ni M National Han Han Han Han Han Han Zhuang Zhuang Zang Sample locaiton Shandong Shandong Jilin Haerbin Shanxi Shanxi Guanxi Guanxi Tibet I11 I12 I13 I14 I15 I16 I17 I18 I19 I20 I21 I22 I23 I24 I25 I26 I27 I28 I29 I30 I31 I10 Ni D Yan Z Piao Y Yan D Liu Z Huang F Su Y Hu R GSM1 GSM2 SBYi1 SBYi2 XYUR1 XYUR2 Yan J HGG21 HGG22 He C SLE4F SLE4M SLE4S1 Zhan D Bulang Bulang Caoxian Dai Han Han Menggu Menggu Miao Miao Yi Yi Weiwuer Weiwuer Dai Han Han Han Han Han Han Zang Yunnan Yunnan Jilin Yunnan Fujian Fujian Heilongjiang Heilongjiang Guizhou Guizhou Sichuan Sichuan Xinjiang Xinjiang Yunnan Guangdong Guangdong Shanghai Shanghai Shanghai Shanghai Tibet age 11 9 37 24 22 8 59 18 30 24 43 17 18 14 14 39 28 Sex M M M M F F M M M M M M M M M M M M M M M M M M F F F M F M M The pooling samples No1. C09 C10 C11 C12 property pool pool pool pool No2. P01 P02 P03 P04 D01 D02 D03 D04 D05 D06 D07 D08 D09 D10 D11 D12 D12 pool pool pool pool pool pool pool pool pool pool pool pool pool P05 P06 P07 P08 P09 P10 P11 P12 P13 P14 P15 P16 P16 Sample Sample locaiton sum Han North Han,South High choleserol Coronary heart Disease SLE Shanxi Guangdong Nanjing 39 Diabetes Ⅰ NIDDM Hypertension Control Hypertension Hypotension Graves' disease Schizophrenia Schizophrenia Affrican European European Shanghai 49 43 239 Shanghai Shanghai Beijing Shanghai Shanghai Henan Henan Liaoning Shanghai Beijing 84 75 96 96 96 36 36 96 200 200 Sex Examples of our Current Work 3 Genetic analysis of Minority population in China and its implication in the origin of Modern human in the East Asia. Three Hypotheses on Modern Human Origin Time (millions of years) 2.0 Homo erectus 1.5 1.0 0.5 0.0 Homo sapiens H. s. sapiens Africa Europe Asia Australia Africa Europe Asia Australia Africa Europe Asia Australia The Formation Of Modern Chinese Populations from microsatelletes evidence Research materials 28 Chinese populations 15 foreign groups as control Basic methods Microsatelates Genotyping and Genescan Neighbor-joining method What is the difference from the past researchers? 1.Strict in samples collecting 2.Marks and analysis methods with foreign 3.Compared samples Sea of Okhotsk 1 2 MONGOLI A 3 4 5North Korea Sea of U.S. S.R. Japan 7 CHINA 8 AFGHANI STAN South Korea JAP AN IRAN NEPAL PAKISTAN BHUTAN INDIA Gulf of Oman BANGLADES H 10 17 11 9 15 12 14 13 16 VI ETNAM BURMA Arabi an Sea LAOS 25 24 KAMP UCHEA Andaman Sea SRI LANKA TAIWAN South China Sea Pacific Ocean East China Sea 19 18 HONG KONG 23 THAI LAND Bay of Beng al 6 20 21 22lippi ne Phi Sea THE PHILI PPI NE S Gulf of Thail and BRUNEI MALAY SI A 26 MALAY SI A SI NGAPORE 27 Indi an Ocean 28 PAPUA NEW GUINEA INDONES IA Coral S ea AUS TRALIA 11 Main conclusions: 1.There are some genetic differences between nationalities in north and south China, but the relations are quite complicated. Main conclusions: 2 . Chinese people’s migration might be from the south to the north. Main conclusions: 3.Modern humans originating in Africa constitute the majority of the current gene pool in East Asia. Sea of Okhotsk MONGOLIA U.S.S.R. Sea of North Korea Japan CHINA South Korea JAPAN AFGHANISTAN IRAN Ocean East NEPAL PAKISTAN INDIA Gulf of China BHUTAN Sea BANGLADESH Oman TAIWAN VIETNAM BURMA LAOS HONG KONG THAILAND Bay of Bengal Philippine Sea South Arabian Sea Pacific China THE PHILIPPINES Sea KAMPUCHEA Andaman Sea SRI LANKA Indian Ocean Gulf of Thailand BRUNEI MALAYSIA MALAYSIA SINGAPORE PAPUA NEW GUINEA INDONESIA Coral Sea AUSTRALIA The Formation Of Modern Chinese Populations From Y chromosomes Evidence. To test the hypotheses of modern human origin in East Asia, Yuehai Ke and Li Jin(6) sampled 12,127 male individuals from 163 populations across Southeast Asia, Oceania, East Asia, Siberia, and Central Asia and typed for three Y chromosome biallelic markers (YAP, M89, and M130) Study on 12,000 Y Chromosomes All the individuals carried a mutation coalesce to another mutation(M168T),which originated in Africa about 35,000 to 89,000 yeas ago. Therefore,the data do not support even a minimal in situ hominid contribution in the origin of anatomically modern humans in East Asia. Conclusion The phylogeny based on microsatellites and Y chromosomes revealed a clear distinction between southern and northern Chinese populations. In both phylogenies with different loci and populations, populations from East Asia always derived from a single lineage indicating the single origin of those populations. The current analysis suggests that the southern populations in East Asia may be derived from the populations in Southeast Asia that originally migrated from Africa and the northern populations were under strong genetic influence from Altaic populations from the north. It is now probably safe to conclude that modern human originated in Africa constitutes majority of the current gene pool in East Asia . Examples of our Current Work 4 GENOME DIVERSITY AND DISEASE Human Origins/Evolution Disease susceptibility “Disease is Part of an Evolutionary Process” Genome diversity research related to diseases G6PD (glucose-6-phosphate dehydrogenase) Deficiency gene rate Dai Lahu Deang Wa Jingpo Hani 0.1610 0.1136 0.2014 0.0821 0.0450 0.0370 Incidence rate of abnormal hemoglobin Achang Jino Deang Jingpo Dai Lisu Aini Bai Lahu Hani Wa 0.4293 0.1625 0.1399 0.1225 0.1212 0.1044 0.1180 0.0479 0.0299 0.0182 0.0182 System lupus erythmatosus is an autoimmune disease, and a complex polygenic disorder Problems for complex traits: Incomplete penetrance Phenocopy Genetic heterogeneity Polygenic inheritance High frequency of mutant alleles Mitochondrial inheritance Anticipation from trinucleotide repeats Imprinting Some conclusions of SLE TNFa1(p=0.0281), TNFc2(p=0.0000) allele frequencies were significantly increased in the SLE group compared to controls. But TNFa2 (p=0.0476), c3(p=0.0043), c4(p=0.0013), d6(p=0.0448) allele frequencies were decreased in the SLE group compared to controls. Meanwhile, we have found the possible new genotypes in Yunnan Han population: TNFc3 (size of fragment is 161bp), TNFc4(163bp), TNFd7(136bp), TNFd8(138bp), TNFe1(99bp). Parkinson’s disease Parkinson’s disease(PD) is the second most common neurodegenerative disorder after Alzheimer’s disease, affecting people seriously. Although many factors, including circumstance, neurotoxin etc, are regarded as probable reasons, genetics analysis in recent years revealed that PD was associated with some genetic factor. V1 Linkage mapping analysis of this PD family Using 400 microsatellite markers to perform whole genome genescanning, and position the rough location of the candidate gene Design a series of primers to position the exact location of gene Detect the mutation of candidate gene and find the genetic reason of PD Long-lived people in Bama Bama in Guangxi province is one of famous long-lived people counties in the world The fifth Chinese census ( in 2000) the number of longevous people in Bama whose age over 100 is up to 74 from 66 in 1990 the proportion of long-lived people, 0.031%, is the highest in the whole world Beautiful Bama The old people of Bama Two Pedigrees of Bama Old People Huang Buhan, male, 105 Huang Mayou, female, 104 Call for international cooperation -Data base and analysis -Compared with foreign samples. -Exchange DNA samples and cell lines. -Cooperation on Diversity and Disease Gene research. Acknowledgements Chinese Natural Science foundation Ministry of Science and Tecnologe Chen Zhu, Chinese Academy of Sciences, Qiang Boqin, Chinese Academy of Medical Sciences Jin Li, Cincinaty University,USA, Li Pu , Harbin Medical University , Xu Jiujin, Institute of Genetics,CAS, Huang Wei, Shanghai 2ed Medical University, Qian Yaping, Chu Zhengtao,Yang Zhaoqing, Yu Jiankun, Institute of Medical Biology,CAMS