Core collection construction of tea plant germplasm in Anhui Province based on genetic diversity analysis using simple sequence repeat markers

The tea plant[Camellia sinensis(L.)O.Kuntze]is an industrial crop in China.The Anhui Province has a long history of tea cultivation and has a large resource of tea germplasm with abundant genetic diversity.To reduce the cost of conservation and utilization of germplasm resources,a core collection needs to be constructed.To this end,573 representative tea accessions were collected from six major tea-producing areas in Anhui Province.Based on 60 pairs of simple sequence repeat(SSR)markers,phylogenetic relationships,population structure and principal coordinate analysis(PCoA)were conducted.Phylogenetic analysis indicated that the 573 tea individuals clustered into five groups were related to geographical location and were consistent with the results of the PCoA.Finally,we constructed a core collection consisting of 115 tea individuals,accounting for 20%of the whole collection.The 115 core collections were considered to have a 90.9%retention rate for the observed number of alleles(Na),and Shannon’s information index(I)of the core and whole collections were highly consistent.Of these,39 individuals were preserved in the Huangshan area,accounting for 33.9%of the core collection,while only 10 individuals were reserved in the Jinzhai County,accounting for 8.9%of the core set.PCoA of the accessions in the tea plant core collection exhibited a pattern nearly identical to that of the accessions in the entire collection,further supporting the broad representation of the core germplasm in Anhui Province.The results demonstrated that the core collection could represent the genetic diversity of the original collection.Our present work is valuable for the high-efficiency conservation and utilization of tea plant germplasms in Anhui Province.

Genetic Diversity Analysis and Constructing Core Collection Based on Phenotypes in Cotton

In that DNA diversity detected nowadays could not mean phenotypic diversity,it is the precondition of breeding project and basic research of crop improvement that genetic diversity analysis and sampling of core collection by phenotypes.Phenotyping and statistic analysis on 9 traits of 92 accessions of cotton germplasm resource from three species（Gossypium hirsutum L.,Gossypium barbadence L.and Gossypium arboreum L.）were conducted.And the statistics（variation coefficient,proportion of special accessions and Shannon-Weaver information index）indicated that initial collection had abundant phenotypic diversity;software NTSYS-pc and the unweighted pair group method of arithmetic（UPGMA）were used for the cluster analysis on genetic similarity coefficient and genetic distance matrix,and the result showed that the genetic relationship among accessions was highly consistent with the pedigree;22 accessions of core collection were selected by software QGAStation,four statistics,such as variance difference percentage（VD%）,mean difference percentage（MD%）,coincidence rate（CR%）and variable rate（VR%）,showed that the genetic diversity of core collection was approximately equal to the initial collection.The results of genetic diversity analysis based on phenotypic data and sampling of core collection would provide reference for breeding projects and basic research.

Assessment on Evaluating Parameters of Rice Core Collections Constructed by Genotypic Values and Molecular Marker Information

Eleven evaluating parameters for rice core collection were assessed based on genotypic values and molecular marke＇ information. Monte Carlo simulation combined with mixed linear model was used to eliminate the interference from environment in order to draw more reliable results. The coincidence rate of range （CR） was the optimal parameter. Mean Simpson index （MD）, mean Shannon-Weaver index of genetic diversity （M1） and mean polymorphism information content （MPIC） were important evaluating parameters. The variable rate of coefficient of variation （VR） could act as an important reference parameter for evaluating the variation degree of core collection. Percentage of polymorphic loci （p） could be used as a determination parameter for the size of core collection. Mean difference percentage （MD） was a determination parameter for the reliability judgment of core collection. The effective evaluating parameters for core collection selected in the research could be used as criteria for sampling percentage in different plant germplasm populations.

Fingerprinting 146 Chinese chestnut(Castanea mollissima Blume)accessions and selecting a core collection using SSR markers

Chinese chestnut is an important nut tree around the world.Although the types of Chinese chestnut resources are abundant,resource utilization and protection of chestnut accessions are still very limited.Here,we fingerprinted and determined the genetic relationships and core collections of Chinese chestnuts using 18 fluorescently labeled SSR markers generated from 146 chestnut accessions.Our analyses showed that these markers from the tested accessions are highly polymorphic,with an average allele number(N_(a))and polymorphic information content(PIC)of 8.100 and 0.622 per locus,respectively.Using these strongly distinguishing markers,we successfully constructed unique fingerprints for 146 chestnut accessions and selected seven of the SSR markers as core markers to rapidly distinguish different accessions.Our exploration of the genetic relationships among the five cultivar groups indicated that Chinese chestnut accessions are divided into three regional type groups:group I(North China(NC)and Northwest China(NWC)cultivar groups),group II(middle and lower reaches of the Yangtze River(MLY)cultivar group)and group III(Southeast China(SEC)and Southwest China(SWC)cultivar groups).Finally,we selected 45 core collection members which represent the most genetic diversity of Chinese chestnut accessions.This study provides valuable information for identifying chestnut accessions and understanding the phylogenetic relationships among cultivar groups,which can serve as the basis for efficient breeding in the future.

Constructing a Core Collection for Maize (Zea mays L.) Landrace from Wuling Mountain Region in China

Based on the genetic clustering from 42 microsatellite （SSR） markers with a combination of their geographic origin and germplasm characteristics, 124 maize landraces from Wuling Mountain region in China were used for constructing a core collection. Four evaluating parameters for maize landrace core collection, including mean difference percentage （MD）, variance difference percentage （VD）, coincidence rate of range （CR）, and variable rate of coefficient of variation （VR）, were assessed With 20 quantitative traits. It was shown that genetic relationships among landraces in Wuling Mountain region had the tendency to associate with their geographic origins. The 124 landraces were clustered into 18 subgroups when the coefficient of genetic similarity （GS） is 0.28. Eighteen landraces, each of which was from one subgroup, were applied to construct the core collection with a sampling percentage of 15%. Comparison of the initial and core collection indicated that there existed no significant differences in most quantitative traits. An average of 6.3 and 6.5 alleles were detected in the initial and core collection, respectively. Mean polymorphism information content in the core collection （0.75） was higher than that in the initial one （0.72）. MD was lesser than 20% and CR was more than 80%. The results showed that the sampling strategy would be feasible for constructing the core collection that well represents the genetic diversity of the initial one.

Strategies on Sample Size Determination and Qualitative and Quantitative Traits Integration to Construct Core Collection of Rice (Oryza sativa)

The development of a core collection could enhance the utilization of germplasm collections in crop improvement programs and simplify their management. Selection of an appropriate sampling strategy is an important prerequisite to construct a core collection with appropriate size in order to adequately represent the genetic spectrum and maximally capture the genetic diversity in available crop collections. The present study was initiated to construct nested core collections to determine the appropriate sample size to represent the genetic diversity of rice landrace collection based on 15 quantitative traits and 34 qualitative traits of 2 262 rice accessions. The results showed that 50-225 nested core collections, whose sampling rate was 2.2%-9.9%, were sufficient to maintain the maximum genetic diversity of the initial collections. Of these, 150 accessions （6.6%） could capture the maximal genetic diversity of the initial collection. Three data types, i.e. qualitative traits （QT1）, quantitative traits （QT2） and integrated qualitative and quantitative traits （QTT）, were compared for their efficiency in constructing core collections based on the weighted pair-group average method combined with stepwise clustering and preferred sampling on adjusted Euclidean distances. Every combining scheme constructed eight rice core collections （225, 200, 175, 150, 125, 100, 75 and 50）. The results showed that the QTT data was the best in constructing a core collection as indicated by the genetic diversity of core collections. A core collection constructed only on the information of QT1 could not represent the initial collection effectively. QTT should be used together to construct a productive core collection.

Method of Constructing Core Collection for Malus sieversii in Xinjiang,China Using Molecular Markers

The method for constructing core collection ofMalus sieversii based on molecular marker data was proposed. According to 128 SSR allele of 109 M. sieversii, an allele preferred sampling strategy was used to construct M. sieversii core collection, using the UPGMA （unweighted pair-group average method） cluster method according to Nei ＆ Li, SM, and Jaccard genetic distances, by stepwise clustering, and compared with the random sampling strategy. The number of lost allele and t-test of Nei＇s gene diversity and Shannon＇s information index were used to evaluate the representative core collections. The results showed that compared with the random sampling strategy, allele preferred sampling strategy could construct more representative core collections. SM, difference for construction of M. sieversii core collection. Jaccard, and Nei ＆ Li genetic distances had no significant SRAP （sequence-related amplified polymorphism） data and morphological data showed that allele preferred sampling strategy was a good sampling strategy for constructing core collection of M. sieversii. Allele preferred sampling strategy combined with SM, Jaccard, and Nei ＆ Li genetic distances using stepwise clustering was the suitable method for constructing M. sieversii core collection.

Analysis on Mineral Element Contents in Associated with Varietal Type in Core Collection of Yunnan Rice

Eight-element contents of 653 unpolished rice samples harvested from Xingping experiment farm, Yunnan Province under the same ecological conditions were analyzed by ICP-AES method. The mineral elements content were closely related to low diversity, high-yielding, and multi-resistance breeding; The K, Mg, Ca and Mn content in high-yielding and resistant varieties were high, and other nutrients such as P, Fe, Zn and Cu were low, which was connected with the heredity and physiological mechanism of mineral nutrients. There is zonal distribution of mineral elements content from Yunnan rice, especially for P, Fe, Zn and Cu co-related with the diversity center, paddy versus upland, glutinous and non-glutinous, glume-hair versus nuda, rice color, rice flavor, soft rice versus non-soft rice, but it did not find any association with indica-japonica types. The results supported the ecological variety group view of 5-grade taxonomic system species-subspecies-ecological groups-ecological variety groups - varietal types' .

Analysis of an Applied Core Collection of Adzuki Bean Germplasm by Using SSR Markers

Genetic diversity of 158 accessions of an applied core collection of adzuki bean （Vigna angularis） and 18 wild genotypes were assessed by using 85 microsatellite markers. With an average of 5.81 alleles per locus, 493 alleles were detected, and their distribution frequencies lower than 5% accounted for 73.02% of the total number. The distributions of alleles between the cultivated and the wild adzuki bean germplasm are different, with a higher allelic diversity in the wild germplasm than that of the cultivated ones. An obvious genetic differentiation was also observed between the wild and the cultivated adzuki beans, and SSR markers may be useful in study identification and classification of them. Among cultivated adzuki bean, the genetic similarity coefficient varied from 0.366 to 0.939. Genetic structure analysis can clearly separate the wild genotypes from the cultivated adzuki bean, and also can divide the cultivated ones into different populations, as these populations are closely agreeable with the ecological regions where they originally grow. The results of this study will be useful in arranging local breeding programs, especially in the aspect of parental combinations or identification of progenies. These SSR markers can also provide important information to explain the genetic relationship between the cultivated and wild adzuki beans, and to accelerate the wild gene resources in broadening the gene pool in breeding program.

Phylogeography and Characteristics of Phosphorus Efficiency of Secondary Core Collection for Rice Landraces in Yunnan Province

[Objective] The paper was to explore the causes of phosphorus(P)efficiency of rice in Yunnan Province,and to provide strategy for ecological and environmental protection.[Method]Using 703 accessions of secondary core collections from 16 prefectures of five regions in Yunnan Province,two treatments of low available P(6.26mg/kg)versus normal P(available P 40mg/kg),and invalid P(available P 0.02 mg/kg)versus normal P(available P 70 mg/kg)were set,and zonal characteristics of phosphorus efficiency and the activation characteristics of invalid P of rice landraces were investigated.[Result] Phosphorus efficiency and the activation characteristics of invalid P in soils from rice landraces of Yunnan Province had the similar identification indexes,viz.the relative indexes of four traits(tillering ability or effective panicle,root weight,biomass,and straw weight)could be the screening indexes of gene type of secondary core collection with phosphorus efficiency,which also reflected the zonal characteristics of phosphorus efficiency and the activation characteristics of invalid P in soils of 16 prefectures among five regions.On the contrary,the relative panicle length,node length under panicle,leaf length,leaf width and plant height could only be the assistant indexes of identification for phosphorus efficiency.There were similar zonal characteristics between phosphorus efficiency and the activation characteristics of invalid P in soils of rice landraces in Yunnan Province.[Conclusion] The study had great importance to the conservation and utilization of biological diversity,which would make contribution to second green revolution of "less input,multiple output,promote health,and protect the environment".

Core Collection of Cassava ( Manihot esculenta Crantz) Germplasm

[Objective] This paper aimed to construct the core collection of cassava germplasm. [Methods] Parameter values of six traits of 161 clones were ana-lyzed and evaluated. [ Results] Minkowski genetic distance was established for cluster analysis of core collection. Preferred sampling method （D 2C5S3） was suit-able for the construction of the core collection of cassava. A total of 25 core collections were obtained, which accounted for 15% of the original germplasm and could represent the genetic diversity and integrity of the original germplasms. Meanwhile, it reflected that the genetic background of the tested cassava germplasm was nar-row and the range of genetic diversity was quite small with genetic redundancy. [ Conclusions] Constructing core collection provided a theoretical foundation for the protection and utilization of cassava germplasms.

Genetic Diversity of Soybean and the Establishment of a Core Collection Focused on Resistance to Soybean Cyst Nematode

Soybean cyst nematode （SCN; Heterodera glycines） Is one of the most Important pests affecting soybean production. The best method of control of SCN is through the development of resistant cultlvars. However, limited progress has been made in soybean breeding In China because most modern cultlvars have no resistance to SCN. The distribution and phenotype of 432 immune or highly resistant Chinese accessions were surveyed and a primary core collection was selected as a representative sample for further analyses. Using evenly distributed simple sequence repeat markers, five selection methods were applied to the primary core collection and the optimal method was chosen to establish a core collection, which consisted of 28 accessions. These encompassed 70.8% of the ailelic variation present in the overall resistant collection. The 28 accessions differed from the reference resistant accessions at the genomlc level, Indicating that Chinese resistant accessions are distinct from known resistant accessions. This applied core collection provides a rational framework for undertaking diversity surveys, using genetic variation for the investigation of complex traits and for the discovery of novel traits.

Simple Sequence Repeat Analysis of Genetic Diversity in Primary Core Collection of Peach(Prunus persica)

In this study, the genetic diversity of 51 cultivars in the primary core collection of peach （Prunus persica （L.） Batsch） was evaluated by using simple sequence repeats （SSRs）. The phylogenetic relationships and the evolutionary history among different cultivars were determined on the basis of SSR data. Twenty-two polymorphic SSR primer pairs were selected, and a total of 111 alleles were identified in the 51 cultivars, with an average of 5 alleles per locus. According to traditional Chinese classification of peach cultivars, the 51 cultivars in the peach primary core collection belong to six variety groups. The SSR analysis revealed that the levels of the genetic diversity within each variety group were ranked as Sweet peach 〉 Crisp peach 〉 Flat peach 〉 Nectarine 〉 Honey Peach 〉 Yellow fleshed peach. The genetic diversity among the Chinese cultivars was higher than that among the introduced cultivars. Cluster analysis by the unweighted pair group method with arithmetic averaging （UPGMA） placed the 51 cultivars into five linkage clusters. Cultivar members from the same variety group were distributed in different UPGMA clusters and some members from different variety groups were placed under the same cluster. Different variety groups could not be differentiated in accordance with SSR markers. The SSR analysis revealed rich genetic diversity in the peach primary core collection, representative of genetic resources of peach.

Genetic characterization of melon accessions in the U.S. National Plant Germplasm System and construction of a melon core collection

Melon(C.melo L.)is an economically important vegetable crop cultivated worldwide.The melon collection in the U.S.National Plant Germplasm System(NPGS)is a valuable resource to conserve natural genetic diversity and provide novel traits for melon breeding.Here we use the genotyping-by-sequencing(GBS)technology to characterize 2083 melon accessions in the NPGS collected from major melon production areas as well as regions where primitive melons exist.Population structure and genetic diversity analyses suggested that C.melo ssp.melo was firstly introduced from the centers of origin,Indian and Pakistan,to Central and West Asia,and then brought to Europe and Americas.C.melo ssp.melo from East Asia was likely derived from C.melo ssp.agrestis in India and Pakistan and displayed a distinct genetic background compared to the rest of ssp.melo accessions from other geographic regions.We developed a core collection of 383 accessions capturing more than 98%of genetic variation in the germplasm,providing a publicly accessible collection for future research and genomics-assisted breeding of melon.Thirty-five morphological characters investigated in the core collection indicated high variability of these characters across accessions in the collection.Genome-wide association studies using the core collection panel identified potentially associated genome regions related to fruit quality and other horticultural traits.This study provides insights into melon origin and domestication,and the constructed core collection and identified genome loci potentially associated with important traits provide valuable resources for future melon research and breeding.

Development of a Core Set from a Large Rice Collection using a Modified Heuristic Algorithm to Retain Maximum Diversity

A new heuristic approach was undertaken for the establishment of a core set for the diversity research of rice. As a result, 107 entries were selected from the 10 368 characterized accessions. The core set derived using this new approach provided a good representation of the characterized accessions present in the entire collection. No significant differences for the mean, range, standard deviation and coefficient of variation of each trait were observed between the core and existing collections. We also compared the diversity of core sets established using this Heuristic Core Collection （HCC） approach with those of core sets established using the conventional clustering methods. This modified heuristic algorithm can also be used to select genotype data with allelic richness and reduced redundancy, and to facilitate management and use of large collections of plant genetic resources in a more efficient way.

Correlation of Plant Morphological and Grain Quality Traits with Mineral Element Contents in Yunnan Rice

Correlations between four grain quality, 24 plant morphological traits and eight element contents of 653 accessions from Yunnan rice were analyzed. P, K, Ca and Mg contents of core collection were closely correlated to the most plant morphological and grain quality traits, and there were highly significant correlations （P 〈0.01） among some traits including P content to number of stems and tillers, K content and amylose content, Ca content and plant height, Mg content and protein content. Mn, Zn, Cu and Fe contents of core collection were closely related to a few traits, such as Fe content and gel consistency （-0.1121^＊＊）, Zn content and seed setting rate （-0.1411^＊＊）, Cu content and number of grains per panicle （-0.1398^＊＊）, Mn content and plant height （-0.2492^＊＊）.

Allelic Variation and Genetic Diversity at Glu-1 Loci in Chinese Wheat (Triticum aestivum L.) Germplasms

Wheat processing quality is greatly influenced by the seed proteins especially the high molecular weight glutenin subunit (HMW-GS) components, the low molecular weight glutenin subunit (LMW-GS) components and gliadin components. Genes encoding the HMW-GS and LMW-GS components were located on the long arms and the short arms of homoeologous group 1 chromosomes, respectively. HMW-GS components in 5 129 accessions of wheat germplasms were analyzed systematically, including 3 459 landraces and 1 670 modern varieties. These accessions were chosen as candidate core collections to represent the genetic diversity of Chinese common wheat ( Triticum aestivum) germplasms documented and conserved in the National Gene Bank. These candidate core collections covered the 10 wheat production regions in China. In the whole country, the dominating alleles at the three loci are Glu-A1b (null), Glu-B1b (7 + 8), and Glu-D1a (2 + 12), respectively. The obvious difference between the land race and the modern variety is the dramatic frequency increase of alleles Glu-A1a (1), Glu-B1c (7 + 9), Glu-B1h (14 + 15), Glu-D1d (5 + 10) and allele cording 5 + 12 subunits in the later ones. In the whole view, there is minor difference on the genetic(allelic)richness between the landrace and the modern variety at Glu-1, which is 28 and 30 respectively. However, the genetic dispersion index (Simpson index) based on allelic variation and frequencies at Glu-A1, Glu-B1 and Glu-D1 suggested that the modern varieties had much higher genetic diversity than the landraces. This revealed that various isolating mechanisms (such as auto-gamous nature, low migration because of undeveloped transposition system) limited the gene flow and exchange between populations of the landraces, which led up to some genotypes localized in very small areas. Modern breeding has strongly promoted gene exchanges and introgression between populations and previous isolated populations. In the three loci, Glu-Bl has the highest genetic diversity , then Glu-D1, while Glu-A1 always keeps the lowest genetic diversity. In the landrace, the three regions with the highest allelic richness are Huanghuai Winter Wheat Region, Northwest Spring Wheat Region and Southwestern Winter Wheat Region. For the bred varieties, the highest allelic richness existed in Southwest Winter Wheat Region, Huanghuai Winter Wheat Region, Low & Middle Branch Winter Wheat Region of Yangtze River. Introduction and utilization of foreign varieties in cross breeding has had great effects on the allelic components and frequency of the three loci, which greatly affected the genetic dispersion index. This has made 'population' of the modern variety quite different from that of the landrace.

Identification of blast-resistance loci through genome-wide association analysis in foxtail millet(Setaria italica (L.)Beauv.)

Blast disease caused by the fungus Magnaporthe grisea results in significant yield losses of cereal crops across the world.To date,very few regulatory genes contributing to blast resistance in grass species have been identified and the genetic basis of blast resistance in cereals remains elusive.Here,a core collection of foxtail millet(Setaria italica)containing 888 accessions was evaluated through inoculation with the blast strain HN-1 and a genome-wide association study(GWAS)was performed to detect regulators responsible for blast disease resistance in foxtail millet.The phenotypic variation of foxtail millet accessions inoculated with the blast strain HN-1 indicated that less than 1.60% of the samples were highly resistant,35.25% were moderately resistant,57.09% were moderately susceptible,and 6.08% were highly susceptible.The geographical pattern of blast-resistant samples revealed that a high proportion of resistant accessions were located in lower latitude regions where the foxtail millet growing season has higher rain precipitation.Using 720000 SNP markers covering the Setaria genome,GWAS showed that two genomic loci from chromosomes 2 and 9 were significantly associated with blast disease resistance in foxtail millet.Finally,eight putative genes were identified using rice blast-related transcriptomic data.The results of this work lay a foundation for the foxtail millet blast resistance biology and provide guidance for breeding practices in this promising crop species and other cereals.

Tendency and foci of nurse practitioners:bibliometric analysis based on the CiteSpaceV

Objective:Nurse practitioners(NPs)have drawn significant attention recently and played a major role in healthcare.We aim to find the evaluation of NPs through published studies and then visualize the research status and hotspots in this field.Methods:All data came from the Web of Science Core Collection,and the data were counted and entered into Excel 2016.The key documents nodes were excavated by analyzing the knowledge network map using Cite Space V software.In this study,these nodes of“author,country,institution,keyword,co-citation(referencecited-authorcited-journal),and grant”were harvested for analysis and comparison.Results:A total of 4912 records,which were published between 2007 and 2018 and pertained to NPs,were retrieved from the Web of Science Core Collection database(Wo SCC)from a diversity of languages.The total and the annual number of publications and citations of these continually increased over time.Most publications were in 2018(618 records).This study involved 8241 authors located in 98 countries and 4557 institutions totally.The United States(2737 records)and the University of Michigan(90 records)dominated in publication frequency.There are 902 journals and 2449 articles with funding support that have been analyzed.Most articles were from JAMA:The Journal of the American Medical Association(1386,IF=47.661),followed by the Journal of Advanced Nursing(1359,IF=2.267),and The New England Journal of Medicine(1109,IF=79.258).The reference“The Role of Nurse Practitioners in Reinventing Primary Care”was co-cited most frequently,which revealed it as the highest landmark article in NP.The top-ranked keyword was“Care,”other than“Nurse practitioner,”which has an ultra-high frequency.Some of the high-frequency keywords represent the significant direction of NPs.Conclusions:NPs are at the crux of health-care delivery and play an important role in providing high-quality nursing.Publications on NPs in Wo SCC have increased notably during the recent years,and have appeared in some journals that have a high impact factor.Research frontiers and developmental trends were revealed by the analysis in this study,which can be used to forecast future research developments in NPs and taken as a reference to choose the right directions by subsequent researchers who wish to use these results.However,the grant support from administration or research institutions is still in need of improvement and the scope of research in NPs should be broadened in the future.

Elemental Content in Brown Rice by Inductively Coupled Plasma Atomic Emission Spectroscopy Reveals the Evolution of Asian Cultivated Rice

The phylogenetic relationship for classification traits and eight mineral elements in brown rice （Oryza sativa L.） from Yunnan Province in China was carried out using microwave assisted digestion followed by inductively coupled plasma atomic emission spectroscopy, and the analytical procedures were carefully controlled and validated. In general, the results show that the mean levels of K, Ca, Mg, Fe and Cu in brown rice for 789 accessions of rice landraces was distinctly lower than that of improved cultivars. They further demonstrate that Ca plays an important role in the differentiation of subspecies indica-japonica, especially to enhance adaptation of cold stress, and that five mineral elements in brown rice enhance the eurytopicity from landrace to improved cultivar. Hierarchical cluster analysis, using average linkage from SPSS software based on eight mineral elements in brown rice, showed that Yunnan rice could be grouped into rice landrace and improved cultivar, with the rice landrace being further clustered into five subgroups, and that, interestingly, purple rice does not cluster with either of the groups. Our present data confirm that indica is the closest relative of late rice and white rice, and that they constitute rice landraces together, whereas japonica is the closest relatives of non-nuda, early-mid and glutinous rice. It is further shown that japonica, non-nuda, early-mid, glutinous, white and red rice might be more primitive than indica, nuda, late, non-glutinous and purple rice, respectively.