Toll like receptor4 (TLR4) gene is conserved over evolution resulting in high degree of homology between species (Jungi et al., 2010). It is a type I transmembrane proteins characterized by an extracellular leucine-rich domain and a cytoplasmic domain referred to as Toll/IL- 1R domain (or TIR domain) because of its homology with cytoplasmic domain of the mammalian interleu- kin1 (Jungi et al., 2010). TLR4 plays a key-role in innate immune system by recognizing conserved molecules on the surface of various microbes. Its extracellular ligand recognition domain then binds to specific pathogen-as- sociated molecular patterns (PAMPs) (Tirumurugaan et al., 2010) and the recognition signals cascade through intracellular domain to initiate signaling events in- cluding translocation of transcription factors, cytokine modulation, and interferon-stimulated gene regulation leading to inflammatory responses and or release of antimicrobial agents (Takeda & Akira, 2003).
ABSTRACT: The most buffaloes in Bangladesh are indigenous in origin. There are 5 populations of buffaloes in Bangladesh. Karyotypic experiment indicated that Bangladesh East population had 48 chromosomes while other populations had 50 chromosomes. Blood protein polymorphism study revealed the existence of polymorphism for 7 loci: albumin, transferrin, hemoglobin-α, hemoglobin-β, carbonic anhydrase, alkaline phosphatase and peptidase-B. Alb X , gene for typical swamp buffalo, was detected in populations of BDE and
The buffalo contributes effectively in the agricultural economy and food security in the countries of the Indian Subcontinent and South East Asia, through meat, milk, leather and labor. It is well known that the buffalo was domesticated very early in history, but when and where is unknown (Cockrill, 1974). The water buffalo emerged in East Asia (Potts 1996) and mainland South East Asia. It spread north and west to China and to the Indian subcontinent (Lau, 1998). The buffalo has been present in the valley of the Indus River in the Indian subcontinent since about 4000-5000 years ago, but there are areas of independent domestication of water buffalo in Mesopotamia and China earlier than this-about 2500-7000 BC (Haynes et al., 1991; Payne, 1991 and Bradley, 2006). Macgregor (1939) classifi ed buffalo into two types according to formal criteria and behavior: the river buffalo in the Indian subcontinent and westerly to the Balkan region and the swamp buffalo in Southeast Asia, India, Nepal and northeast to the valley of the Yangtze River in China. Barker et al. (1997) was the fi rst to analyze thegeneticdiversity of buffalo breeds in South Asia using protein coding spatial microsatellites. They noted a clear distinction between these two types: river and marsh buffaloes, the latter being raised mainly in the swamps of Southeast Asia, and this distinctiojn was confi rmed later by Zhang GENETICDIVERSITY AND CONSERVATION OF ANIMAL GENETIC RESOURCES IN
The majority of Syria’s goat population of 2.29 million heads consists of indigenous goats which are distributed all over the country (FAOSTAT, 2011) and raised for multipurpose uses. The economic importance of small ruminants has been increasing in Syria in recent years due to the erratic rainfall and related risk of crop failures. Besides, indigenous goat populations are known in general for heat tolerance, disease resistance, mothering and walking abilities, and the ability to efficiently metabolize low quality feeds (Trail and Gregory, 1984). Thus, indigenous goats are very valuable genetic resources adapted and suited for low-inputs-outputs agricultural production systems of the developing countries like Syria. The Mediterranean countries, namely Lebanon, Syria and Cyprus are considered as the main goat milk and cheese producer next to India (Dubeuf et al., 2004) and the Shami (Damascus) goat is well appreciated for its high milk yield and twinning ability. Recognizing the value of the Shami goats, the Syrian Ministry of Agriculture and Agrarian reform established seven Shami goats’ improvement and conservation research and development centers in representative provinces of the country to maintain and improve this unique goat breed. Thegenetic relationships and differentiation between Shami and other native goat populations available in Syria have not yet been characterized and established in a way to contribute to the declared aim of the Food and Agriculture Organization (FAO) of the United Nations to preserve thegeneticdiversity of domestic animals including goats.
To investigate whether some of the exon sequence changes are unique to Indonesian accessions, data on 80,630 SNPs that could be mapped to the 20 soybean chromosomes were compared with SNP data obtained from resequencing 31 Chinese accessions (Lam et al., 2010). There were 57,009 SNPs that matched the SNPs from the Chinese accessions, while 23,621 were unique to the five Indonesian cultivars. These mutation data could comprise a valuable resource for dissecting genetic adaptation to the tropical climate of Indonesia. Using these mutation data, we then assessed thegeneticdiversity of the five cultivars compared with the Chinese accessions, which were expected to have greater diversity as they originated in the area where soybean was initially domesticated and some wild accessions were also present among these 31 acces- sions. A neighbour-joining tree based on 1000 bootstrap replicates was then constructed from the polymorphism data of 1400 genic SNPs that exhibited polymorphism among the Chinese and Indonesian accessions and had a sequencing depth of at least three reads in all the five Indonesian cultivars (Fig. 1). As expected, the five Indonesian accessions were clustered relatively close to each other within the cluster of cultivated accessions from China, even in the case of the Tambora cultivar, which is a recent introduction from the Philippines. The closest relative to Tambora is C16, a Taiwanese cultivar that originated from a Japanese cultivar and is also the closest relative to two other Indonesian cultivars, Malabar and Davros. Malabar is the result of a recent breeding programme that crossed superior local cultivars, while Davros was purified from landraces commonly planted in Garut District (West Java). B3293, a landrace from Kediri (East Java), belongs to a different group and was shown to be most similar to C17, a landrace from Sichuan, in Southwest China.
One of thegenetic resources of local cattle which the potential to utilize, is local cattle from Ciamis district which is the region with the third highest cattle population in West Java, following Tasikmalaya and Sumedang (Disnak Jabar, 2011). Ciamis local cattle has small body size with low average daily gain. However they have good body composition and efficient in their reproduction. The introgession of artificial insemination (AI) in the district of Ciamis is quite intensive, therefore local cattle genetic resources could be lost, due to crossbreeding program. Diwyanto (2005) stated that thegeneticdiversity of Indonesian local cattle has significance role in the development of livestock, as a resource of geneticdiversity that is needed in the assembly superior breed, lead to increase their productivity.
Numerous examples in previous studies showed that species with a small geographic range generally maintain less ge- netic diversity than geographically widespread species (Gitzendanner and Soltis, 2000; Wu et al., 2004; Zheng et al., 2012). However, our data suggest that the taxa restricted to narrow populations (P. tabulaeformis f. shekanensis and P. henryi) were more diverse than P. tabulaeformis and P. massoniana, two species that are widely distributed. Hamrick and Godt (1989) concluded that the primary factors in ﬂ uencing thegeneticdiversity of plant populations include breeding system, distri- bution range, and habit. Plant species with higher genetic variation are usually characterized by long life span, wide geographic distribution, predominant outcrossing, anemophily, good fecundity, and a late stage of succession. Thus, the higher level of geneticdiversity observed within P. tabulaeformis f. shekanensis and P. henryi may be related to their late stage of succession. Additionally, in this paper, each taxon, no matter its distribution, selected only in one population may be another reason.
The research about Geneticdiversity analysis of the passion fruit (Passiflora spp.) in north Sumatera based on RAPD markers has been done in Genetic Laboratory and Integrated Laboratory, University of North Sumatera. The objective of this study was to characterize thegeneticdiversity of Passiflora sp. collection by RAPD marker. RAPD analysis was done to 31 passion fruit (Passiflora sp.) accessions that collected from 4 regional is region HUMBAHAS, North Tapanuli, Simalungun, and Karo that represented 4 species (P. edulis, P. ligularis, P. quadrangularis, P. foetida) from genus of Passiflora using 4 random primers (selected from 7 random primers). The result of electrophoresis showed 73 reproducible polymorphic bands (98%) are ranging in size from 250 bp to 2500 bp. Thegenetic similarity showed coefficients ranged from 0,8 to 0,97 based on Unweight Pair- Group Method Aritchmatic and Numerical Taxonomy (UPGMA) and Multivariate System (NTSYS) version 2.11a computer program,. The result revealed high levels of variation within and among species. Cluster analysis showed that grouping of passion fruit occurs by area collecting of the sample. Geographical proximity and similarity of the area where passion fruit had been collecting and based on the color of the fruit do not guarantee thegenetic relationship of passion fruit by RAPD.
Thegeneticdiversity of global livestock populations is declining . Our study examined this trend in global pig populations. We analyzed the mtDNA D-Loop for haplotypes in 4434 samples, and found 334 haplotypes, including 166 shared haplotypes found in all sequences. We also analyzed geneticdiversity by basic parameters (Hd, Pi and K), and principal component analysis. Previous studies established that the level of genetic variation among Asian pigs was lower than that among European domestic pigs [7,11], and the re- sults of this study are consistent with those ﬁ ndings. The global pig population is approximately one billion, two thirds of this popu- lation is found in Asia, with the majority found in China . Geneticdiversity is low in these pigs, due to commercial hybridization. Chinese indigenous pigs show some unfavorable traits such as slow growth, small body weight, low dressing percentage and high back fat thickness. To improve production, these populations are crossed with commercial pigs (Duro, Landrace and Yorkshire) . Di- versity of indigenous porcine populations is, therefore, impacted by commercial breeds. There are a considerable number of pigs in Vietnam and India , and most of them were indigenous pigs. Geneticdiversity in these countries was high. Europe and the Caucasus have approximately one ﬁ fth of the global pig population, while America has an additional 15% . Geneticdiversity is rela- tively high in these populations. No analysis was done for African pig populations due to a lack of data. Based on principle component analysis, Fz ranged from 3.200 e 3.200, indicating that European, American and Oceanian pigs had a similar level of diversity which was slightly higher than the Asian pig population. This is consistent with the analysis of the parameters Pi and K. The majority of populations/breeds focused in 1.200 e 1.200, indicating a low level of geneticdiversity in pig populations globally. In conclusion, the mtDNA diversity observed underscores the signi ﬁ cance of the indigenous breeds/populations as an important genetic resource.
Genes related to starch synthesis and the metabolism contribute to a variety of physicochemical properties that determine the eating/cooking qualities of rice. Our previous study suggested that a set of molecular markers was able to estimate the eating quality of japonica rice. The present study reports thegeneticdiversity of 22 japonica rice varieties based on markers corresponding to starch synthesizing genes. The mean of the polymorphic information content (PIC: 0.135) value and thediversity index (0.171) indicated a low geneticdiversity in these varieties. The phylogenetic tree clearly demonstrated three main clusters: 1) cluster I contained seven varieties with similar physicochemical properties; 2) cluster II only showed a Japanese variety, Koshihikari, and 3) cluster III included the most Korean varieties (14 varieties). This phylogenetic analysis did not completely represent the physicochemical properties differentiation of the japonica varieties, although it did reveal an initial clue to the close relationship between Korean rice and the Japanese and Chinese varieties. Notably, these markers were also able to identify a premium japonica rice. The molecular markers and information concerning thegenetic relationship would be useful in improving the japonica rice along with its starch quality of in breeding program.
The purpose of this study was to determine genetic variation and phylogenetic relationships of the cattle Bali-Bali and Bali-Lombok on variations of the cytochrome b gene of mitochondrial DNA. The benefits of this research is to provide scientific information of thegeneticdiversity and phylogenetic Bali’s cattle in Bali and Lombok compared with the ancestor Banteng (Bos javanicus) based on cytochrome b mitochondrial gene.
Thegeneticdiversity plays a crucial role in supporting many plant breeding program, including the rubber trees. Such geneticdiversity may be estimated either at phenotype or molecular levels. Unlike those phenotype-based characterizations, molecular marker-based evaluations of geneticdiversity are more accurate since the molecular markers are not affected by environmental factors. Simple sequence repeats (SSR) or microsatellites is one of the markers widely distributed throughout the nuclear genome of eukaryotes (Bhargava & Fuentes, 2010). SSR marker is highly polymorphic and often use as genetic markers for population genetic analysis (Guichoux et al., 2011). Several genetic analysis has been done using SSR markers, such as in coconut (Larekeng, Maskromo, Purwito, Matjik, & Sudarsono, 2015; Maskromo et al., 2015) and oil palm (Tinche, Asmono, Dinarti, & Sudarsono, 2014). Scientists have also done the evaluation of rubber tree geneticdiversity analysis using RAPD or SSR markers (Besse et al., 1994; Saha, Roy, & Nazeer, 2005; Lam, Thanh, Chi, & Tuy, 2009; Gouvêa, Rubiano, Chioratto, Zucchi, & de Souza Gonçalves, 2010). Diversity analysis using SSR markers is more beneicial than using other dominant markers since SSR markers can differentiate the homozygous and the heterozygous individuals and exhibit high polymorphism. Moreover, SSR markers are highly reproducible and transferable among related species, and they can differentiate closely related accessions (Mantello,
The main objective of this study was to determine, using mi- crosatellite markers, thegeneticdiversity and the relationship of two major camel ecotypes inhabiting the eastern (Butana) and western (Darfur) regions of Sudan. Butana and Darfur are considered the major entities of camel populations in Su- dan (Eisa and Mustafa, 2011). All 12 analysed loci displayed a large range of polymorphisms, and so their use should re- duce the danger of overestimating genetic variability (Wim- mers et al., 2000). They produced low F ST values, which in turn are useful for cluster analysis and capable of indicating genetic variation in terms of observed alleles (Rosenberg et al., 2001).
In this study, the number of alleles (n a ), expected (H E ) and observed (H O ) heterozygosity, F IS and PIC values for each locus and population as well as the average values for the loci and populations are given in Table 2. Totally 103 alleles were detected in the whole sample and the number of alleles varied from 3 (loci CSSM57, ETH003) to 10 (locus CSSM47) with the mean number of alleles being 5.15 per locus (Table 2). The mean number of alleles observed in populations differed slightly: the minimum 3.70 was observed in THR and the maximum 4.35 was in BSR. The polymorphic information content (PIC) was calculated for each marker and ranged from 0.14 (locus CSSM32) to 0.820 (locus CSSM47), which has the highest number of alleles per locus in the present study. The average PIC in our populations was 0.4945. Nine microsatellites (ILSTS033, CSSM43, CSRM60, CSSM47, BMC1013, CSSM29, CSSM36, ILSTS030 and ETH121), having a PIC value higher than the threshold of 0.5 (Botstein et al. 1980, Seyedabadi et al. 2006), seemed to be highly informative and can be used in quantifying thegeneticdiversity and also in paternity studies in Turkey.
Several studies have reported that DNA microsatellite marker have been widely used to study geneticdiversity in Spanish sheep (Arranz et al., 2001), European sheep (Peter et al., 2007), meat type sheep in China (Chen et al., 2009) and Ganjam sheep (Arora et al. 2010). Based on the lack of genetic information about garut sheep of fighting and meat types, purbalingga sheep, batur sheep and jember sheep populations as Indonesian local sheep, so microsatellite markers became one of the reasons where this research was conducted to determine thegeneticdiversity in Indonesian sheep population especially garut sheep of fighting type, garut sheep of meat type, purbalingga sheep, batur sheep and jember sheep populations.
Germplasms resources of wild strawberry are rich in Motuo country of Tibet, China. In this study, we assessed geneticdiversity of seventy wild strawberry germplasms from different geographical regions using simple sequence repeat (SSR) markers. Thegeneticdiversity of wild strawberry was demonstrated by 189 polymorphic SSR-PCR bands obtained using ten selective primers. Additionally, the average polymorphic information content (PIC), total gene diversity and population diversity were 0.941, 0.331 and 0.214, respectively. At the population level, variation of strawberry accessions among population was higher than that within population. Based on arithmetic mean (UPGMA) dendrogram method, all samples were clustered into 6 groups and two subgroups. Combined with the results of UPGMA and Principle coordinate analysis, wild strawberry accessions tended to group by geographic origin. Thus, these ﬁndings will beneﬁt for the protection and exploitation of wild strawberry, and provide theoretical basis for further study in the origin and phylo- genetic systematics of wild strawberry.
Establishment of seed orchard is aimed at producing good quality seeds which is an important activity for breeding program. Seed orchard is also a base population, thus its geneticdiversity is depending on its design and composition (provenance, family and individual tree). Selection of an individual tree in seed orchard is needed for the enhancement of retaining good-character trees. However, selection of individual tree can change thegeneticdiversity of seed orchard, and the degrees to which thegeneticdiversity will change depend on the used selection methods. In order to investigate the effects of selection methods, 4 simulations of selection methods based on height, diameter and stem performance of individual trees were used. The differences among the 4 methods were the ranking of individual trees those selected, and families and provenances those have been represented. Seedling seed orchard of Acacia mangium in Wonogiri, Central Java was used as materials.
over a period of one year. In total, 40 diferent spoligotypes were found, corresponding to a genotypic diversity of 40.0%. his percentage was higher than the 19.1% found by Ouassa et al. in previously treated cases in Cˆote d’Ivoire but was quite similar to 35.1% obtained on thegeneticdiversity in a mixed population of new and previously treated cases in Rwanda [15, 16]. A genotypic diversity of 49.0% was reported in 2005 among new cases in Cotonou, the biggest city in Benin, suggesting that genetic diversities were similar among new and previously treated cases . However, the previous study among new cases was carried out 10 years ago and distribution of spoligotypes in new cases might have changed over time. In addition, the national igure might be diferent from what was obtained in Cotonou.
Alhamdulillahirobbil alamin, penulis lafadkan atas segala rahmat dan karunia dari ALLAH SWT yang telah diberikan kepada penulis selama melakukan penelitian hingga penyelesaian penulisan disertasi ini. Disertasi yang berjudul Keragaman Genetik dan Mikroevolusi Pyricularia grisea Asal Rumput memuat hasil penelitian tentang keragaman cendawan blas pada beberapa spesies rumput yang tumbuh di sekitar pertanaman padi, dan perubahan genetik cendawan blas yang mengalami pergantian inang secara buatan. serta hubungan filogenetik antara cendawan blas pada rumput Digitaria ciliaris, Panicum repens, dan padi. Hasil yang diperoleh diharapkan dapat berkontribusi informasi pada manajemen penyakit blas pada padi di Jawa Barat. Bagian dari disertasi ini telah disajikan pada Seminar Sains III di Bogor pada bulan November 2010 yang diselenggarakan oleh FMIPA IPB dengan MIPAnet, dengan judul Keragaman Genetik Hasil Pergantian Inang Pyricularia grisea Asal Rumput Digitaria ciliaris. Selain itu sebuah artikel telah dipublikasikan di Jurnal Microbiology Indonesia 2011 berjudul Diversity of SCAR Markers of Pyricularia grisea Isolated from Digitaria ciliaris Following Cross Infection to Rice, 5(1):1-8. Melalui tulisan ini, penulis menyampaikan terima kasih dan penghargaan yang sebesar-besarnya kepada Dr.Ir. Utut Widyastuti, M.Si. selaku ketua komisi pembimbing, Dr.Ir. Gayuh Rahayu, MS., Prof.Dr.Ir. Alex Hartana, M.Sc. selaku anggota komisi pembimbing, atas segala curahan waktu, pikiran, nasihat dan arahan selama penelitian dan penulisan hasil disertasi. Terimakasih kepada bapak Dr.Ir. Muhammad Jusuf (Alm) atas bimbingan serta nasihat kepada penulis. Penulis juga menyampaikan terima kasih kepada seluruh jajaran pimpinan Institut Pertanian Bogor, yaitu Rektor yang telah mengizinkan penulis melanjutkan studi program doktor. Dekan Sekolah Pascasarjana IPB, Dr.Ir. Dedy Duryadi Solihin, DEA selaku Ketua Program Studi Biologi Sekolah Pascasarjana, Ketua Departemen Biologi FMIPA, dan Direktur Pusat Penelitian Sumberdaya Hayati dan Bioteknologi (PPSHB) yang telah memfasilitasi studi S3 ini.