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Genetic Diversity and allelic Frequency of Selected Thai and Exotic Rice Germplasm Using SSR Markers

Rice science 2019年第6期26卷 393-403页

作者： Wanwarang PATHAICHINDACHOTE Natjaree PANYAWUT Kannika SIKAEWTUNG Sujin PATARAPUWADOL Amorntip MUANGPROM Center for Agricultural Biotechnology Kasetsart University Kamphaeng Saen Campus Nakhon Pathom 73140 Thailand Center of Excellence on Agricultural Biotechnology Science and Technology Postgraduate Education and Research Development Office Office of Higher Education Commission Ministry of Education Bangkok 10900 Thailand Department of Agricultural Sciences Faculty of Agriculture Natural Resources and Environment Naresuan University Phitsanulok 65000 Thailand National Center for Genetic Engineering and Biotechnology Thailand Science Park Pathum Thani 12120 Thailand Department of Plant Pathology Faculty of Agriculture at Kamphaeng Saen Kasetsart University Kamphaeng Saen Campus Nakhon Pathom 73140 Thailand

A collection of 167 Thai and exotic rice accessions was subjected for evaluation of genetic diversity and assessment of relationship by simple sequence repeat (SSR) markers. Among a total of 49 SSR markers, 13 markers distributing over 12 rice chromosomes showed clear polymorphic band patterns, and they were selected for genetic assessment. A total of 110 alleles were detected with an average of 8.46 alleles per locus. The averages of gene diversity, heterozygosity and polymorphic information content were 0.59, 0.02 and 0.56, respectively. The unweighted-pair group method with arithmetic averages (UPGMA) clustering analysis was performed for genetic distance, and phylogenetic tree was constructed. The result showed that this rice collection was divided into two major groups, classified as japonica and indica subspecies. Within the japonica group, temperate japonica and tropical japonica subgroups can be clearly separated. Three-dimensional principal component analysis projection and model-based population structure analysis showed consistent clustering results with two major groups of UPGMA analysis, supporting the classification of japonica and indica subspecies. The indica allelic frequency was also investigated to provide an indicative guide for breeders to overcome the practical problems on sterility of inter-subspecies hybrid offspring. This rice collection and information obtained in this study will be useful for rice breeding programs.

关键词： rice genetic diversity indica japonica allelic frequency simple sequence repeat

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Variation in allelic frequencies at loci associated with kernel weight and their effects on kernel weight-related traits in winter wheat

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The Crop Journal 2019年第1期7卷 30-37页

作者： Teng Li Hongwei Liu Chunyan Mai Guangjun Yu Huili Li Lingzhi Meng Dawei Jian Li Yang Yang Zhou Hongjun Zhang Hongjie Li National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop Sciences Chinese Academy of Agricultural Sciences Xinxiang Innovation Center for Breeding Technology of Dwarf-Male-Sterile Wheat Zhaoxian Experiment Station Shijiazhuang Academy of Agricultural and Forestry Sciences Institute of Agricultural Science The Fourth Division of the Xinjiang Production and Construction Corps

Knowledge of allelic frequencies at loci associated with kernel weight and effects on kernel weight-related traits is crucial for yield improvement in wheat. Kernel weight-related traits were evaluated in 200 Chinese winter wheat cultivars(lines) grown at the Xinxiang Experimental Station, Chinese Academy of Agricultural Sciences, Xinxiang in Henan Province, for three consecutive years from 2014 to 2016. Alleles associated with kernel weight at nine loci, TaCKX6-D1, TaCwi-A1, TaCWI-4A, TaGS1a, TaGS5-A1, TaGS3-3A, TaGW2-6A, TaSus2-2B, and TaTGW6-A1, were determined for all cultivars(lines). ANOVA showed that genotypes, years and their interactions had significant effects on thousand-kernel weight(TKW), kernel length(KL) and kernel width(KW). The overall mean frequencies of alleles conferring high and low TKW at the nine loci were 65.9% and 33.4%, with the ranges of 37.0%–85.0% and 13.5%–63.0% for single loci. The frequencies of high-TKW alleles were over 50.0% at eight of the loci. Genotypes at each locus with the high-TKW allele had higher TKW than those with the low-TKW allele. The high-TKW allele Hap-H at the TaSus2-2B locus can be preferably used to increase grain yield due to its high TKW(49.32 g). A total of 18 main allelic combinations(ACs) at nine loci were detected. Three ACs(AC1–AC3) had significantly higher TKW than AC6 with high-TKW alleles at all nine loci even though they contained some low-TKW alleles. This indicated that other loci controlling kernel weight were present in the high-TKW cultivars. This work provides important information for parental selection and marker-assisted selection for breeding.

关键词： allelic frequency allelic variation Functional markers Triticum aestivum

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An Exploratory Study on allelic Diversity for Five Genetic Loci Associated with Floral Organ Development in Rice

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American Journal of Plant Sciences 2015年第12期6卷 1973-1980页

作者： Alok Priya Soumya Prakash Das Sayani Goswami Malay Kr. Adak Debal Deb Narottam Dey Department of Biotechnology Visva-Bharati Santiniketan-731235 West Bengal India Plant Physiology and Plant Molecular Biology Research Unit Department of Botany University of Kalyani Kalyani-741235 West Bengal India Basudha Barrackpore Kolkata-700120 West Bengal India

allelic diversity for five genetic loci (DL, FON4, OsMADS24, OsMADS45 and Spw1) associated with floral organ development were investigated among a small heterogeneous rice population which included one wild species (O. rufipogon Griffiths), one indigenous less popular natural floral organ mutant (O. sativa var. indica cv. Jugal), one indigenous normal line (O. sativa var. indica cv. Bhutmoori) and one improved high yielding line (O. sativa var. indica cv. IR 36). Detailed spikelet morphology showed that var. Jugal had variable number (1 - 3) of carpels within a single spikelet which was unique and resulted in variable (1 - 3) number of kernels within a single matured spikelet (grain). The genomic DNA of each investigated line was amplified with primer sequences designed from the selected genetic loci and the derived polymorphism profiles were used for study of allelic diversity for the studied loci. The derived genetic distances among the rice lines were used for dendrogram construction. In constructed dendrogram, the mutant genotype (Jugal) showed highest similarity with the wild rice (O. rufipogon) instead of the rice lines. To verify this finding, the genomic DNA of each studied line was also amplified with four SSR loci, tightly linked to saltol QTL, mapped to rice chromosome 1. The amplified products were screened for polymorphism and another dendrogram was constructed to reveal the genetic distance among the lines for selected salt tolerance linked SSR loci. In SSR derived dendrogram, the wild rice (O. rufipogon) got totally separated from the all three rice genotypes though all the studied four lines showed equal sensitivity for salt sensitivity in a physiological screening experiment. From the combined experiment, it can be concluded that genetic architecture of floral organ development loci in var. Jugal may have some uniqueness which is not present in normal rice but common to O. rufipogon, a species which is regarded as immediate progenitor of present day

关键词： Rice Multiple Kernel Floral Organ Number Mutant Rice Microsatellite allelic Diversity

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A study of the relationship between frequency of allelic deletion of chromosome 17p and late-stage colorectal carcinoma

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Journal of Medical Colleges of PLA(China) 1998年第2期13卷 79-82页

作者：季晨阳季丹

Late stage colorectal carcinoma is very complicated in its molecular mechanisms. One hundred andnine cases of colorectal carcinomas were analyzed with RFLP method for the allelic deletion of chromosome 17short arms (ADCC17p) In this study. The results showed that frs(luency of allelic deletion of chromosome 17short arms (FADC17P) in Dukes’ D stage (95 % ) was higher than those in Dukes’ A, B. C stages (54% 68% ); Fisher’s exact test P 0. 05). Therefore, it is considered that ADC17p is an important diagnosticmarker of late stage colorectal carcinomas, and indicates a poor prognosis.

关键词： late stage colorectal carcinomas allelic deletion P53 gene

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Molecular characterization of secaloindoline genes in introduced CIMMYT primary hexaploid triticale

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The Crop Journal 2017年第5期5卷 430-437页

作者： Hongmei Liu Xiaobian Zhou Xiangnan Li Junying Chen Dangqun Cui Feng Chen Agricultural College National Key Laboratory of Wheat and Corn Crop Collaborative Innovation Center of Henan Grain Crops Henan Agricultural University

In order to widen gene germplasm for kernel hardness in triticale, 60 synthetic hexaploid triticales were tested by the single kernel characterization system(SKCS) and secaloindoline alleles were identified by sequencing. Phenot^ing showed that frequencies of soft, mixed and hard genotypes were 43.3%, 48.3%, and 8.4%, respectively. Genotyping identified three known secaloindoline-a alleles and four known secaloindoline-b alleles. Three new Sina-Rl alleles were designated Sina-Rld, Sina-Rle and Sina-Rlf. Compared to Sina-Dlc, Sina-Rld showed four point mutations causing changes in four amino acids, Sina-Rle had one point mutation causing an alanine to glycine substitution, and Sina-Rlf possessed five point mutations but produced the same amino add sequence as Sina-Rld. Two new Sinb-Rl alleles were discovered and designated Sinb-Rle and Sinb-Rl/. Compared to Sinb-Rla, Sinb-Rle possessed a triplet-code insertion and four point mutations causing a cysteine insertion and two amino acid substitutions, and Sinb-Rl/possessed three point mutations causing a cysteine insertion and a change of arginine to *** of hardness index with secaloindoline alleles indicated t±iat SKCS of the Sina-Rld genotype was significantly lower than that of Sina-Rle, and Sinb-Rle was significantly lower than that of the Sinb-Rld genotype. A total of eight allelic combinations of secaloindoline genes were identified; Sma-Rld/Sinb-Rle and Sina-Rle/Sinb-Rld were relatively prevalent in the triticales surveyed. The results provide valuable information for further use of these germplasms in triticale breeding program due to the diverse polymorphism in secaloindoline genes.

关键词： Kernel hardness allelic variation Secaloindoline genes Hexaploid triticale

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Wx^lv、the Ancestral Allele of Rice Waxy Gene

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Molecular Plant 2019年第8期12卷 1157-1166页

作者： Changquan Zhang Jihui Zhu Shengjie Chen Xiaolei Fan Qianfeng Li Yan Lu Min Wang Hengxiu Yu Chuandeng Yi Shuzhu Tang Minghong Gu Qiaoquan Liu Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding College of AgricultureYangzhou UniversityYangzhou 225009China Co-lnnovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province Yangzhou UniversityYangzhou 225009China

In rice grains,the Waxy (Wx) gene is responsible for the synthesis of amylose,the most important determinant for eating and cooking *** effects of several Wx alleles on amylose content and the taste of cooked rice have been ***,the relationship between artificial selection and the evolution of various Wx alleles as well as their distribution remain *** we report the identification of an ancestral allele,Wx^lv,which dramatically affects the mouthfeel of rice grains by modulating the size of amylose *** demonstrated that WF originated directly from wild rice,and the three major Wx alleles in cultivated rice (Wx^b,Wx^a,and Wx^in) differentiated after the substitution of one base pair at the functional *** data indicate that the Wx^lv allele played an important role in artificial selection and *** findings also shed light on the evolution of various Wx alleles,which have greatly contributed to improving the eating and cooking quality of rice.

关键词： Oryza sativa Waxy eating and cooking quality allelic variation artificial selection

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Deep genotyping of the gene GmSNAP facilitates pyramiding resistance to cyst nematode in soybean

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The Crop Journal 2019年第5期7卷 677-684页

作者： Yu Tian Bo Liu Xuehui Shi Jochen C.Reif Rongxia Guan Ying-hui Li Li-juan Qiu The National Key Facility for Crop Gene Resources and Genetic Improvement(NFCRI)/Key Lab of Germplasm Utilization(MOA) Institute of Crop SciencesChinese Academy of Agricultural Sciences100081 BeijingChina Department of Breeding Research Leibniz Institute of Plant Genetics and Crop Plant Research(IPK)GaterslebenGermany

Soybean cyst nematode(SCN)is a highly destructive *** soybean host genome harbors at least two major genes for resistance(rhg1 and Rhg4),as well as a minor locus(SCN3-11).In the present study,a splicing site in GmSNAP11,the potential causal gene of SCN3-11,was identified by comparison of the GmSNAP11 cDNA sequences generated from resistant and susceptible soybean *** sequence information was used to design a codominant CAPS marker,GmSNAP11-2565,which was used to genotype a panel of 209 soybean accessions varying with respect to SCN *** of the effect of the haplotypes formed by GmSNAP11-2565 and another large-effect(nonsynonymous)locus,GmSNAP11-2307,previously identified in GmSNAP11,revealed linkage disequilibrium(P<0.0001)between the two loci,suggesting that GmSNAP11-2565 could be used as a marker for ***11-2565 was accordingly used,along with established markers for GmSNAP18(rhg1)and GmSHMT(Rhg4),to characterize the panel *** mean SCN female index of accessions carrying only the GmSNAP11 allele associated with resistance(20.3%)was higher than that associated with accessions carrying alleles for resistance at both GmSNAP11 and GmSNAP18(12.4%),while the index for accessions carrying alleles for resistance at all of GmSNAP11,GmSNAP18,and GmSHMT was very low(1.9%).Selection on all three markers was effective for maintaining a high level of resistance to SCN race 3.

关键词： SCN α-SNAP allelic combination Marker-assisted selection(MAS) Haplotype analysis

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Novel alleles among soybean Bowman-Birk proteinase inhibitor gene families

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Science China(Life Sciences) 2008年第8期51卷 687-692页

作者： WANG YuePing1,2, CHEN XiongTing2 & QIU LiJuan1 1 National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Crop Germplasm & Biotechnology(MOA)/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 10008, China 2 Institute of Tropical Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China National Key Facility for Crop Gene Resources and Genetic Improvement Key Laboratory of Crop Germplasm & Biotechnology (MOA)/Institute of Crop Science Chinese Academy of Agricultural Sciences Beijing China Institute of Tropical Biotechnology Chinese Academy of Tropical Agricultural Sciences Haikou China

Trypsin inhibitors have been found in various animals, plants and *** were two types of trypsin inhibitors in soybean including Bowman-Birk protease inhibitors(BBI) and Kunitz in-hibitors(KTI).The different BBI genes from wild soybean(***) and cultivated soybean(***) formed a multigene *** constructed a cDNA library of cultivar 'SuiNong 14' seed at the R7 growth stage using the SMART *** contigs or singletons were highly homologous to soy-bean protease *** of 5, 35, 8 and 9 were highly homologous to BBI family members BBI-A1, BBI-A2, BBI-C and BBI-D, *** analyses showed there were novel allelic varia-tions among the 4 BBI members in SuiNong *** on the comparison of soybean seed cDNA li-braries from different developmental stages, it was apparent that the expression of trypsin inhibitors increased during seed development in *** analysis of BBI gene sequences among dicotyledonous and monocotyledonous plants demonstrated that these genes shared a common pro-genitor.

关键词： soybean trypsin inhibitor Bowman-Birk proteinase inhibitor Kunitz trypsin inhibitor allelic variation

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Polymorphisms of chemokine receptors and its ligand alleles influencing genetic suscepti-bity to HIV-1 infection in eight ethnic groups in Chinese mainland

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Chinese Science Bulletin 2001年第12期46卷 1019-1023页

作者： WANG Fusheng JIN lei LIU Mingxu HONG Weiguo SHI Hong LEI Zhouyun WANG Jiming DU Qingyou HOU Jing ZHANG Bing JIANG Jiandong WANG Yue LI Yueqi XU Anlong HUANG Honglian LIU Fajun Division of Biological Engineering Department of Out-patientsBeijing Institute of Infectious DiseaseBeijing Hospital of Infectious DiseaseBeijing 100039China Laboratory of Molecular Immunoregulation Division of Basic SciencesNational Cancer InstituteFCRDCMD 21702-1201USA Division of Medical Oncology Mount Sinai Medical SchoolNew YorkNY 10029USA Key Laboratory for Molecular Biology Academy of Medical ScienceZhongshan UniversityGuangzhou 510275China Kashi Health and Anti-Epidemic Center KashiXinjiang Uygur Autonomous RegionXinjiang 844001China

Limited genetic information is available concerning the polymorphisms of HIV-1 resistant genes in indigenous Chinese populations. The aim of this study is to identify the allelic frequencies of the chemokine and chemokine receptor genes in the Chinese mainland. Genomic DNA samples extracted from whole blood of 2318 subjects were analyzed by using PCR or PCR/restriction fragment length polymorphism (RFLP) assays, and further confirmed by direct DNA sequencing. Higher frequencies of mutant CCR2-64I (19.15%-28.79%) and SDF1-3’A (19.10% -29.86%) alleles were found in subjects of 8 ethnic groups in the Chinese mainland. In contrast, the △32 mutation in CCRS gene occurs at a very low frequency (0.0016, n=1287) in Han population. A relatively high frequency of CCR5-wt/△32 heterozygotes was observed in Uygurian and Mongolian populations. No A32 mutation allele was detected in Tibetan and other 4 ethnic groups in Yunnan Province. There was no CCR5-m303 mutation in subjects of any ethnic group in the Chinese

关键词： HIV-1 coreceptors polymorphism allelic frequency mutation.

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NDRG2 gene copy number is not altered in colorectal carcinoma

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World Journal of Clinical Oncology 2017年第1期8卷 67-74页

作者： Anders Lorentzen Cathy Mitchelmore Eucaryotic Cell Biology Department of Science and Environment Roskilde University

AIM To investigate if the down-regulation of N-myc Downstream Regulated Gene 2(NDRG2) expression in colorectal carcinoma(CRC) is due to loss of the NDRG2 allele(s).METHODS The following were investigated in the human colorectal cancer cell lines DLD-1, Lo Vo and SW-480: NDRG2 mRNA expression levels using quantitative reverse transcriptionpolymerase chain reaction(qRT-PCR); interaction of the MYC gene-regulatory protein with the NDRG2 promoter using chromatin immunoprecipitation; and NDRG2 promoter methylation using bisulfite ***, we performed qPCR to analyse the copy numbers of NDRG2 and MYC genes in the above three cell lines, 8 normal colorectal tissue samples and 40 CRC tissue *** As expected, NDRG2 mRNA levels were low in the three colorectal cancer cell lines, compared to normal *** MYC protein interacted with the NDRG2 core promoter in all three cell *** addition, the NDRG2 promoter was heavily methylated in these cell lines, suggesting an epigenetic regulatory *** gene copy numbers of NDRG2 were observed in the three cell *** the colorectal tissues, one normal and three CRC samples showed partial or complete loss of one NDRG2 *** contrast, the MYC gene was amplified in one cell line and in more than 40% of the CRC *** Our study suggests that the reduction in NDRG2 expression observed in CRC is due to transcriptional repression by MYC and promoter methylation, and is not due to allelic loss.

关键词： N-myc downstream-regulated gene 2 Colorectal carcinoma MYC Tumor suppressor allelic loss Gene amplification Copy number

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