Nuclear microsatellites reveal the genetic architecture and breeding history of tea germplasm of East Africa (original) (raw)
Africa is one of the key centers of global tea production. Understanding the genetic diversity and relationships of cultivars of African tea is important for future targeted breeding efforts for new crop cultivars, specialty tea processing, and to guide germplasm conservation efforts. Despite the economic importance of tea in Africa, no research work has been done so far on its genetic diversity at a continental scale. Twenty-three nSSRs and three plastid DNA regions were used to investigate the genetic diversity, relationships, and breeding patterns of tea accessions collected from eight countries of Africa. A total of 280 African tea accessions generated 297 alleles with a mean of 12.91 alleles per locus and a genetic diversity (H S) estimate of 0.652. A STRUCTURE analysis suggested two main genetic groups of African tea accessions which corresponded well with the two tea types Camellia sinensis var. sinensis and C. sinensis var. assamica, respectively, as well as an admixed " mosaic " group whose individuals were defined as hybrids of F2 and BC generation with a high proportion of C. sinensis var. assamica being maternal parents. Accessions known to be C. sinensis var. assamica further separated into two groups representing the two major tea breeding centers corresponding to southern Africa (Tea Research Foundation of Central Africa, TRFCA), and East Africa (Tea Research Foundation of Kenya, TRFK). Tea accessions were shared among countries. African tea has relatively lower genetic diversity. C. sinensis var. assamica is the main tea type under cultivation and contributes more in tea breeding improvements in Africa. International germplasm exchange and movement among countries within Africa was confirmed. The clustering into two main breeding centers, TRFCA, and TRFK, suggested that some traits of C. sinensis var. assamica and their associated genes possibly underwent selection
2016
Africa is one of the key centers of global tea production. Understanding the genetic diversity and relationships of cultivars of African tea is important for future targeted breeding efforts for new crop cultivars, specialty tea processing, and to guide germplasm conservation efforts. Despite the economic importance of tea in Africa, no research work has been done so far on its genetic diversity at a continental scale. Twenty-three nSSRs and three plastid DNA regions were used to investigate the genetic diversity, relationships, and breeding patterns of tea accessions collected from eight countries of Africa. A total of 280 African tea accessions generated 297 alleles with a mean of 12.91 alleles per locus and a genetic diversity (H S) estimate of 0.652. A STRUCTURE analysis suggested two main genetic groups of African tea accessions which corresponded well with the two tea types Camellia sinensis var. sinensis and C. sinensis var. assamica, respectively, as well as an admixed "mosaic" group whose individuals were defined as hybrids of F2 and BC generation with a high proportion of C. sinensis var. assamica being maternal parents. Accessions known to be C. sinensis var. assamica further separated into two groups representing the two major tea breeding centers corresponding to southern Africa (Tea Research Foundation of Central Africa, TRFCA), and East Africa (Tea Research Foundation of Kenya, TRFK). Tea accessions were shared among countries. African tea has relatively lower genetic diversity. C. sinensis var. assamica is the main tea type under cultivation and contributes more in tea breeding improvements in Africa. International germplasm exchange and movement among countries within Africa was confirmed. The clustering into two main breeding centers, TRFCA, and TRFK, suggested that some traits of C. sinensis var. assamica and their associated genes possibly underwent selection Wambulwa et al. Genetic Architecture of African Tea during geographic differentiation or local breeding preferences. This study represents the first step toward effective utilization of differently inherited molecular markers for exploring the breeding status of African tea. The findings here will be important for planning the exploration, utilization, and conservation of tea germplasm for future breeding efforts in Africa.
Genetic improvement of tea for both health and economic benefit requires proper genetic characterization of sequence variation present in tea accession especially those conserved in the ex-situ genebanks. Here, we studied the genetic variation and population structure of 376 tea germplasm at Rwebitaba Tea Research Centre (RTRC), a tea research station with the largest collections of tea germplasm in East Africa. The study was conducted using 8480 (22.7%) diversity array technology (DArT) SNP markers. These markers had a high call rate of 77% with mean polymorphic information content (P.I.C) of 0.12 and minor allelic frequency of 0.08. The expected heterozygosity (He) varied from 0.05 to 0.15 while the observed heterozygosity (Ho) varied from 0.01 to 0.26. The overall inbreeding coefficient (FIS) was 0.45, with some populations showing a high level of outcrossing (F IS = − 0.035). Analysis of molecular variance revealed a high within-population variance (88.9%) showing weak genetic differentiation between populations (PhiPT = 0.111). Structure analysis showed the presence of eight clusters, with all sub-populations highly admixed except for a few tea clones such as Ch-06 and Ch-07. Phylogenetic analysis confirmed the clustering, showing interrelatedness between different tea genotypes, which will facilitate the selection of parents for increased genetic gain and breeding efficiency in tea breeding. In general, the genetic diversity of tea genotypes is relatively low, with high variation within the existing tea populations. These results showed that the existing variation can be exploited for the development of unique tea genotypes in Uganda.
Scientific reports, 2017
Despite the highly economic value of tea in Africa, its genetic and geographic origins remain largely unexplored. Here we address this by collecting 439 samples across 11 countries in Africa and Asia to investigate the origin and genepool composition of African tea based on 23 nuclear microsatellites loci (nSSRs) and three cpDNA intergenic spacer regions. Our results indicated that the African tea represents a potpourri originating from multiple introductions over time. The nSSR analysis revealed that the majority (79%) of tea accessions collected in Africa belong to Indian Assam tea which have likely originated from India and/or Sri Lanka. The patterns of nSSR variation also showed that Chinese Assam tea is genetically distinct from Indian Assam tea, and has rarely been used in African tea breeding efforts since only 4% of the African tea accessions possessed this genotype. We found a total of 22 cpDNA haplotypes, which grouped into three main geographic clades that were concordant...
Genetic structure and diversity of India hybrid tea
The most important evolutionary event in the success of commercial tea cultivation outside China in *30 countries came about by the origin of India hybrid tea in India, derived from the extensive spontaneous hybridization that took place between the Assam type tea growing in the forest regions of Assam, North-East India and China type tea introduced from China in *1875 to many regions of North-East India. The release of an enormous pool of vigorous and highly variable plants of India hybrid tea in North-East India was a significant step forward for the origin and evolution of tea as a highly successful crop plant. The 1,644 accessions and clones of India hybrid tea, representatives of known 15 morphotypes, were screened by 412 AFLP markers amplified by 7 AFLP primer pair combinations. All the 412 genetic loci were polymorphic across the 1,644 accessions and clones. The analysis was done with distance (PCoAand NJ) methods, and the STRUCTURE (Bayesian) model. Both PCoA and NJ analysis clustered 1,644 tea accessions and clones into six major groups with one group in each, constituted mostly by China hybrid, Assam China hybrid and Assam hybrid morphotypes, of distinct genetic identity.No group was exclusive for any particular morphotype. The accessions and clones belonging to morphotypes, Assam type, Assam hybrid, China hybrid and China Cambod were distributed in all the groups. It is the Assam type/ Assam hybrid morphotypes which exhibit much broader genetic variability than in China type/China hybrid/Cambod type/Cambod hybrid morphotypes. The STRUCTURE analysis inferred 16 populations (K = 16), for which the greatest values of probability were obtained.Nine of the16 clusterswere constituted by the tea accessions and clones of ‘pure’ ancestry. The remaining clusters were of ‘mixed’ ancestry. This analysis provides evidence that the accessions and clones of the same morphotype are not always of same genetic ancestry structure. The tea accessions and clones obtained from outside North-East India shared the same groups (distance method) and clusters (STRUCTURE model) which were constituted by North-East India accessions. The present study also demonstrates very narrow genetic diversity in the commercial tea clones vis-a `-vis the profound genetic diversity existing in the tea accessions. These clones were distributed in hardly two of the six groups in NJ tree. The identified 105 core accessions and clones, capturing 98% diversity, have their origin from almost all groups/subgroups of NJ tree.
Plant Science, 2003
Amplified Fragment Length DNA Polymorphism (AFLP) analysis of 49 tea cultivars from south India produced a total number of 1555 unambiguous polymorphic amplified DNA fragments. The dendrogram derived by unweighted pair group method with arithmetic mean algorithm (UPGMA) analysis and the PCO plot drawn using principal component analysis revealed that all these tea cultivars could be clearly distinguished into three distinct groups viz., Assam, China and Cambod as well as an intermediate. Among the populations characterized, the Chinary type showed a maximum diversity index of 0.612 and the minimum of 0.285 was observed within the Assam type. Genetic distance was maximum (0.946), between Assam and Cambod and minimum (0.852) between Assam and China. More than 90% similarity as observed between the cultivars UPASI-22 and UPASI-23. Affinity of each cultivar towards the populations was determined using the similarity index. Analysis and comparison of AFLP fragments revealed distinct segregation of all the cultivars into their respective groups, except UPASI-18 and UPASI-24. Studies on diversity assessment of south Indian tea cultivars using AFLP fingerprinting revealed that the present day commonly grown south Indian tea germplasm has narrow genetic diversity (B/37.76) among the cultivars necessitating a sustained effort to preserve tea germplasm resources and the development of superior varietal material through wide genetic crosses.
TAG Theoretical and Applied Genetics, 1997
AFLP markers were successfully employed to detect diversity and genetic differentiation among Indian and Kenyan populations of tea (Camellia sinensis (L.) O. Kuntze). Shannon's index of diversity was used to partition the total phenotypic variation into between and within population components. On average, most of the diversity was detected within populations, with 79% of the variation being within and 21% being between populations of Indian and Kenyan tea. A dendrogram constructed on the basis of band sharing distinctly separated the three populations of tea into China type (sinensis), Assam type (assamica) and Cambod type (assamica ssp. lasiocalyx) in a manner consistent with the present taxonomy of tea, the known pedigree of some of the genotypes and their geographical origin. Principal coordinate (PCO) analysis grouped Assam genotypes both from India and Kenya supporting the suggestion that the Kenyan clones have been derived from collections made in this region. The China types were more dispersed on the PCO plot which is a reflection of wider genetic variation. As would be expected, clones collected from the same region exhibited less overall genetic variation. AFLP analysis discriminated all of the tested genotypes from India and Kenya, even those which cannot be distinguished on the basis of morphological and phenotypic traits.
AFLP-Based Genetic Diversity Assessment of Commercially Important Tea Germplasm in India
Biochemical Genetics, 2010
India has a large repository of important tea accessions and, therefore, plays a major role in improving production and quality of tea across the world. Using seven AFLP primer combinations, we analyzed 123 commercially important tea accessions representing major populations in India. The overall genetic similarity recorded was 51%. No significant differences were recorded in average genetic similarity among tea populations cultivated in various geographic regions (northwest 0.60, northeast and south both 0.59). UPGMA cluster analysis grouped the tea accessions according to geographic locations, with a bias toward China or Assam/Cambod types. Cluster analysis results were congruent with principal component analysis. Further, analysis of molecular variance detected a high level of genetic variation (85%) within and limited genetic variation (15%) among the populations, suggesting their origin from a similar genetic pool.
Tea genetic resources in Sri Lanka: Collection, Conservation and Appraisal
At the Tea Research Institute of Sri Lanka conservation aspects on tea germplasm in ex-situ gene bank as living collection was initiated in 1986. Currently, over 600 accessions are being maintained in field gene bank and efforts have been taken to characterize, evaluate and utilize them in the tea breeding program. This paper highlights the significant achievements in the areas of germplasm collection, conservation, characterization and evaluation and their use in tea breeding program giving prominence to the cost effective complementary strategies adopted in germplasm conservation and holistic approaches followed in germplasm characterization to facilitate managerial activities. Over the years, the methods for detecting genetic diversity have expanded from analysis of discrete morphological variants, to biochemical approaches and to co-efficient of pedigree analysis to methods based on DNA markers. This kind of an approach, where genetic diversity assessment is supplemented with a ...
Genetic Diversity Analysis of Eighteen Tea (Camellia sinensisL.) Clones of Bangladesh ThroughRAPD
Using 20 decamer random primers molecular characterization of 18 tea (Camellia sinensis L.) clones of Bangladesh was made. All the primers showed significant amplification in PCR analysis. A total of 755 bands was produced in all the 18 tea clones with an average of 37.75 RAPD bands per primer. Among all the bands 97.41% were polymorphic in nature. The molecular size of the amplified DNA fragments ranged from 250 to 5000 bp. Ten unique bands were amplified from the genome of the 18 tea clones. The values of pairwise genetic distance ranged from 24.0 to 59.0 indicating the presence of a wide range of genetic diversity. The highest genetic distance 59 was found between the clone BT16 and BT2, whereas the lowest (24.0) between BT18 and BT5. The dendrogram based on Nei's genetic distance was constructed using un-weighted Pair Group of Arithmetic Mean (UPGMA) segregating the 18 tea clones into two major clusters: BT9 and BT13 in cluster 1 and the remainder of 16 clones in cluster 2. Cluster 2 is further subdivided into many sub-clusters. Cluster analysis revealed that while the genotype BT5 is closely related to BT18, BT1 and BT2 showed similarity with BT8. Genotypes BT1 and BT13 were widely diverse genetically. Genetic Diversity Analysis of Eighteen Tea Clones 197 Biswas MS, Akhond AAY, Alamin M, Khatun M and Kabir MR (2009) Genetic relationship among ten promising eggplant varieties using RAPD markers. Plant Tissue Cult. & Biotech. 19(2): 119-126. Chen YP, Cao-Jia S, Miao Y, Cao JS and Ye WZ (2000) Analysis of genetic polymorphisms in vegetable crops of Brassica campestris by RAPD markers. J. Zhejiang University. Agric. Life Sci. 26: 131-136. Datta J and Lal N (2011) Characterization of genetic diversity in Cicer arietinum L. and Cajanus cajan L. Millspaugh using random amplified polymorphic DNA and simple sequence repeat markers. Genom. and Quant. Genet. 3: 30-41. Dos Santos JB, Nienhuis J, Skroch P, Tivang J and Slocam (1994) Comparison of RAPD and RELP genetic markers in determining genetic similarity in Brassica oleracea L. genotypes. TAG. 87: 909-915. Doyle JJ and Doyle JL (1987) A rapid DNA isolation procedure from small quantities of fresh leaf tissues. Phytochem. Bull. 96: 11-15. El-Hady EAAA, Haiba AAA, EL-Hamid NRA and Rizkalla AA (2010) Phylogenetic diversity and relationships of some tomato varieties by electrophoretic protein and RAPD analysis. J. Amer. Sci. 6(11): 434-441. Ezekiel CN, Nwangburuka CC, Ajibade OA and Odebode AC (2011) Genetic diversity in 14 tomato (Lycopersicon esculentum Mill.) varieties in Nigerian markets by RAPD-PCR technique. Afr. J. Biotechnol. 10(25): 4961-4967. Gherardi M, Mangin B, Goffinate B, Bonnet D and Huguet T (1998) A method to measure genetic distance between allogamous population of alfalfa (Medicago sativa) using RAPD molecular markers. TAG 96: 406-412. Goodrich WJ, Cook RJ and Morgan AG (1985) The application of electrophoresis to the charecterization of cultivars Vicia faba L. Fabis Newsletter 13:8. Gubba A and Sivparsad BJ (2008) Isolation and molecular characterization of tomato spotted wilt virus (TSWV) isolates occurring in South Africa. Afr. J. Agri. Res. 3(6): 428 -434. Gul S, Ahmed H, Khan IA and Alam M (2007) Assessment of genetic diversity in tea genotypes through RAPD primers. Pakistan J. Biol. Science. 10(15): 2609-2611. Jorge S and Pedroso MC (2003) Genetic Differentiation of Portuguese Tea Plant using RAPD Markers. Hort Science 38(6): 1191-1197. Kaundan SS, Zhyvoloup A and Park Y (2000) Evaluation of the genetic diversity among elite tea accessions using RAPD markers. Euphytica. 115: 7-16. Kidwell KK, Austinand DF and Osborn TC (1994) RFLP evaluation of nine Medicago accessions representing the original germplasm source of North American alfalfa cultivars. Crop Sci. 34: 230-236. Lai J, Yang W and Hisao J (2001) An assessment of genetic relationship in cultivated tea clones and native wild tea in Taiwan using RAPD and ISSR markers. Bot. Bull. Acad. Sin. 42: 93-100.