Genetic dissection of grain traits in Yamadanishiki,an excellent sake-brewing rice cultivar

Key message

The grain traits of Yamadanishiki, an excellent sake-brewing rice cultivar in Japan, are governed by multiple QTLs, namely, a total of 42 QTLs including six major QTLs.

Abstract

Japanese rice wine (sake) is produced using brewing rice (Oryza sativa L.) that carries traits desirable for sake-brewing, such as a larger grain size and higher white-core expression rate (WCE) compared to cooking rice cultivars. However, the genetic basis for these traits in brewing rice cultivars is still unclear. We performed analyses of quantitative trait locus (QTL) of grain and days to heading over 3 years on populations derived from crosses between Koshihikari, a cooking rice, and Yamadanishiki, an excellent sake-brewing rice. A total of 42 QTLs were detected for the grain traits, and the Yamadanishiki alleles at 16 QTLs contributed to larger grain size. Two major QTLs essential for regulating both 100-grain weight (GWt) and grain width (GWh) were harbored in the same regions on chromosomes 5 and 10. An interaction was noted between the environment and the QTL associated with WCE on chromosome 6, which was detected in two of 3 years. In addition, two QTLs for WCE on chromosomes 3 and 10 overlapped with the QTLs for GWt and GWh, suggesting that QTLs associated with grain size also play an important role in the formation of white-core. Despite differences in the rate of grain growth in both Koshihikari and Yamadanishiki across 2 years, the WCE in Yamadanishiki remained consistent, thus demonstrating that the formation of white-core does not depend on grain filling speed. These data can be informative for programs involved in breeding better cooking and brewing rice cultivars.

     

Genome-wide haplotype changes produced by artificial selection during modern rice breeding in Japan

During the last 90 years, the breeding of rice has delivered cultivars with improved agronomic and economic characteristics. Crossing of different lines and successive artificial selection of progeny based on their phenotypes have changed the chromosomal constitution of the ancestors of modern rice; however, the nature of these changes is unclear. The recent accumulation of data for genome-wide single-nucleotide polymorphisms (SNPs) in rice has allowed us to investigate the change in haplotype structure and composition. To assess the impact of these changes during modern breeding, we studied 177 Japanese rice accessions, which were categorized into three groups: landraces, improved cultivars developed from 1931 to 1974 (the early breeding phase), and improved cultivars developed from 1975 to 2005 (the late breeding phase). Phylogenetic tree and structure analysis indicated genetic differentiation between non-irrigated (upland) and irrigated (lowland) rice groups as well as genetic structuring within the irrigated rice group that corresponded to the existence of three subgroups. Pedigree analysis revealed that a limited number of landraces and cultivars was used for breeding at the beginning of the period of systematic breeding and that 11 landraces accounted for 70% of the ancestors of the modern improved cultivars. The values for linkage disequilibrium estimated from SNP alleles and the haplotype diversity determined from consecutive alleles in five-SNP windows indicated that haplotype blocks became less diverse over time as a result of the breeding process. A decrease in haplotype diversity, caused by a reduced number of polymorphisms in the haplotype blocks, was observed in several chromosomal regions. However, our results also indicate that new haplotype polymorphisms have been generated across the genome during the breeding process. These findings will facilitate our understanding of the association between particular haplotypes and desirable phenotypes in modern Japanese rice cultivars.     

Quantitative and molecular analyses reveal a deep genetic divergence between the ancient medicinal rice (Oryza sativa) Njavara and syntopic traditional cultivars

We analysed 76 accessions of the medicinal and nutritive rice (Oryza sativa) landrace Njavara (Shashtika in Sanskrit) and 67 traditional cultivars of Kerala state using phenotypic traits and microsatellite markers. Multivariate analyses of 13 quantitative phenotypic traits revealed two distinct clusters, the Njavara accessions and the traditional cultivars (Qst = 0.4753). Njavara accessions belonging to the same morphotype were clustered together, although no specific pattern could be deciphered from the clustering of traditional cultivars. A total of 222 alleles were generated at the 24 microsatellite loci, with a mean number of 4.42 and 6.623 alleles per locus and a mean gene diversity (He) of 0.479 and 0.596 in Njavara and traditional cultivars, respectively. Different diversity analyses clearly separated Njavara and traditional cultivars from each other. As with the phenotypic analysis, Njavara accessions clustered according to their morphotypes, but the topology of the two dendrograms were different. However, the clustering pattern of traditional cultivars in genotypic dendrogram was inconsistent with that of phenotypic dendrogram. The scented rice cultivars formed a distinct cluster while the remaining traditional cultivars were clustered according to their photosensitivity. Significant (P < 0.0000) partitioning of molecular diversity was recorded between Njavara and traditional cultivars (Fst = 0.4293), within Njavara types (Fst = 0.5616) and traditional cultivars (Fst = 0.2546). The results indicate that Njavara is a cryptic variant within the traditional rice gene pool in Kerala. The study provided valuable information on the genetic structure and population differentiation of traditional rice cultivars in Kerala, which are relevant in breeding and conservation.     

Genetic diversity in cultivars and landraces of Oryza sativa subsp. indica as revealed by AFLP markers.

Genetic diversity among 49 Indian accessions of rice (Oryza sativa subsp. indica), including 29 landraces from Jeypore, 12 modern cultivars, and 8 traditional cultivars from Tamil Nadu, was investigated using AFLP markers. In total, nine primer combinations revealed 664 AFLPs, 408 of which were found to be polymorphic. The percentage of polymorphic AFLPs was approximately the same within the cultivars and landraces. Similar results were obtained when genetic diversity values were estimated using the Shannon-Weiner index of diversity. Genetic diversity was slightly higher in the modern cultivars than in the traditional cultivars from Tamil Nadu. Among the landraces from Jeypore, the lowland landraces showed the highest diversity. The present study showed that the process of breeding modern cultivars did not appear to cause significant genetic erosion in rice. Cluster analysis and the first component of principle component analysis (PCA) both showed a clear demarcation between the cultivars and landraces as separate groups, although the genetic distance between them was narrow. The modern cultivars were positioned between the landraces from Jeypore and the traditional cultivars from Tamil Nadu. The second component of PCA further separated medium and upland landraces from lowland landraces, with the lowland landraces found closest to the traditional and modern cultivars.     

Genetic diversity and population structure of a diverse set of rice germplasm for association mapping

Germplasm diversity is the mainstay for crop improvement and genetic dissection of complex traits. Understanding genetic diversity, population structure, and the level and distribution of linkage disequilibrium (LD) in target populations is of great importance and a prerequisite for association mapping. In this study, 100 genome-wide simple sequence repeat (SSR) markers were used to assess genetic diversity, population structure, and LD of 416 rice accessions including landraces, cultivars and breeding lines collected mostly in China. A model-based population structure analysis divided the rice materials into seven subpopulations. 63% of the SSR pairs in these accessions were in LD, which was mostly due to an overall population structure, since the number of locus pairs in LD was reduced sharply within each subpopulation, with the SSR pairs in LD ranging from 5.9 to 22.9%. Among those SSR pairs showing significant LD, the intrachromosomal LD had an average of 25–50 cM in different subpopulations. Analysis of the phenotypic diversity of 25 traits showed that the population structure accounted for an average of 22.4% of phenotypic variation. An example association mapping for starch quality traits using both the candidate gene mapping and genome-wide mapping strategies based on the estimated population structure was conducted. Candidate gene mapping confirmed that the Wx and starch synthase IIa (SSIIa) genes could be identified as strongly associated with apparent amylose content (AAC) and pasting temperature (PT), respectively. More importantly, we revealed that the Wx gene was also strongly associated with PT. In addition to the major genes, we found five and seven SSRs were associated with AAC and PT, respectively, some of which have not been detected in previous linkage mapping studies. The results suggested that the population may be useful for the genome-wide marker–trait association mapping. This new association population has the potential to identify quantitative trait loci (QTL) with small effects, which will aid in dissecting complex traits and in exploiting the rich diversity present in rice germplasm.     

Historical changes in population structure during rice breeding programs in the northern limits of rice cultivation

Key message

The rice local population was clearly differentiated into six groups over the 100-year history of rice breeding programs in the northern limit of rice cultivation over the world.

Abstract

Genetic improvements in plant breeding programs in local regions have led to the development of new cultivars with specific agronomic traits under environmental conditions and generated the unique genetic structures of local populations. Understanding historical changes in genome structures and phenotypic characteristics within local populations may be useful for identifying profitable genes and/or genetic resources and the creation of new gene combinations in plant breeding programs. In the present study, historical changes were elucidated in genome structures and phenotypic characteristics during 100-year rice breeding programs in Hokkaido, the northern limit of rice cultivation in the world. We selected 63 rice cultivars to represent the historical diversity of this local population from landraces to the current breeding lines. The results of the phylogenetic analysis demonstrated that these cultivars clearly differentiated into six groups over the history of rice breeding programs. Significant differences among these groups were detected in five of the seven traits, indicating that the differentiation of the Hokkaido rice population into these groups was correlated with these phenotypic changes. These results demonstrated that breeding practices in Hokkaido have created new genetic structures for adaptability to specific environmental conditions and breeding objectives. They also provide a new strategy for rice breeding programs in which such unique genes in local populations in the world can explore the genetic potentials of the local populations.     

Analysis of genetic diversity and population structure of rice cultivars from Korea, China and Japan using SSR markers

A total of 29 simple sequence repeat (SSR) markers were used to analyze the genetic diversity of 150 accessions of cultivated rice (Oryza sativa L.) from Korea, China, and Japan. A total of 375 alleles were detected with an average of 12.9 per locus. The averaged values of gene diversity and polymorphism information content (PIC) for each SSR locus were 0.7001 and 0.6683, respectively. Alleles per locus in Korean rice were 8.8, whereas 8.1 and 7.2 alleles per locus were found in Chinese and Japanese rice, respectively. The mean gene diversity in Korean, Chinese, and Japanese rice was 0.6058, 0.6457, and 0.5174, respectively, whereas the mean PIC values for each SSR locus were 0.5759, 0.6138, and 0.4881, respectively. The genetic diversity of the Korean and Chinese cultivars was higher than that of the Japanese cultivars, and the genetic diversity ofjaponica was higher than that ofindica. The model-based structure analysis revealed the presence of three subpopulations, which was basically consistent with clustering based on genetic distance. An AMOVA analysis showed that the between-population component of genetic variance was less than 22% in contrast to 78% for the within-population component. The overallFST value was 0.2180, indicating a moderate differentiation among groups. The results could be used for designing effective breeding programs aimed at broadening the genetic bases of commercially grown varieties.     

Genetic Diversity and Population Differentiation of Liaoning Weedy Rice Detected by RAPD and SSR Markers

Weedy rice refers to populations of usually annual Oryza species that diminish farmer income through reduction of grain yield and lowered commodity value at harvest. The genetic diversity and population genetic structure of weedy rice in Liaoning Province were studied by RAPD and SSR markers. The results indicate that the level of genetic diversity of Liaoning weedy rice is very low, with polymorphic loci being only 3.70% (RAPDs) and 47.62% (SSRs). On the other hand, high genetic differentiation was found among populations, in particular between two regions (Shenyang and Dandong), with Fst values of 0.746 (RAPDs) and 0.656 (SSRs), suggesting that more than two thirds of the genetic variation resides among regions. Combined with our investigations of cultural traditions, the low level of genetic diversity in Liaoning Province is attributed to its narrow genetic background enhanced by exchanges of cultivar seeds, whereas the high genetic differentiation between the two regions is most likely the result of different founding parents and gene flow from local rice varieties to weedy rice. The rice cultivars in the two regions are all local varieties and are different genetically. A comparison of the two marker systems demonstrates that SSR is more informative and powerful in terms of the assessment of genetic variability, although both RAPD and SSR provide useful genetic information on weedy rice.     

Molecular evaluation of genetic diversity and association studies in rice (<Emphasis Type="BoldItalic">Oryza sativa</Emphasis> L.)

In the present study, we tested rice genotypes that included un(der)exploited landraces of Tamil Nadu along with indica and japonica test cultivars to ascertain their genetic diversity structure. Highly polymorphic microsatellite markers were used for generating marker segregation data. A novel measure, allele discrimination index, was used to determine subpopulation differentiation power of each marker. Phenotypic data were collected for yield and component traits. Pattern of molecular differentiation separated indica and japonica genotypes; indica genotypes had two subpopulations within. Landraces were found to have indica genome, but formed a separate subgroup with low linkage disequilibrium. The landraces further separated into distinct group in both hierarchical clustering analysis using neighbour-joining method as well as in the model based population structure analysis. Japonica and the remaining indica cultivars formed two other distinct groups. Linkage disequilibrium observed in the whole population was considerably reduced in subpopulations. Low linkage disequilibrium of landforms suggests their narrow adaptation in local geographical niche. Many population specific alleles could be identified particularly for japonica cultivars and landraces. Association analysis revealed nine marker-trait associations with three agronomic traits, of which 67% were previously reported. Although the testing landraces together with known cultivars had permitted genomewide association mapping, the experiment offers scope to study more landraces collected from the entire geographical region for drawing more reliable information.     

Microsatellites and microsynteny in the chloroplast genomes of Oryza and eight other Gramineae species

Primer pairs flanking ten chloroplast microsatellite loci, originally identified in Oryza sativa cv Nipponbare, were evaluated for amplification and allelic diversity using a panel of 13 diverse cultivars of rice (O. sativa), 19 accessions of wild rice (three O. officinalis, five O. latifolia, five O. minuta, four O. australiensis, one O. brachyantha and one O. ridleyi) and eight other Gramineae species (maize, teosinte, wheat, oat, barley, pearl millet, sorghum and sugarcane). Amplified products were obtained for all samples at nine out of ten loci. Among the rice cultivars, the number of alleles per locus ranged from one to four, with monomorphic patterns observed at five loci. The average polymorphism information content (PIC) value at the other five (polymorphic) loci was 0.54 among the 13 cultivars. When wild rice and the other Gramineae species were compared based on the proportion of shared alleles, their phylogenetic relationships were in agreement with previous studies using different types of markers; however, the magnitude of the differences based on chloroplast microsatellites underestimated the genetic distance separating these divergent species and genera. A sequence-based comparison of homologous regions of the rice and maize chloroplast genomes revealed that, while a high level of microsynteny is evident, the occurrence of actively evolving microsatellite motifs in specific regions of the rice chloroplast genome appears to be mainly a species or genome-specific phenomenon. Thus the chloroplast primer pairs used in this study bracketed mutationally active microsatellite motifs in rice but degenerate, interrupted motifs or highly conserved, mutationally inert motifs in distantly related genera. Received: 17 March 1999 / Accepted: 11 November 1999     

Genealogical analysis of the diversity of spring barley cultivars released in former Czechoslovakia and modern Czech Republic

Genealogical analysis was employed in studying the time course of changes in genetic diversity of spring barley cultivars released in former Czechoslovakia and the modern Czech Republic. Cultivars from different regions proved to significantly differ in the distribution of dominant ancestor contributions, suggesting a specificity of original ancestors to different cultivation conditions. A comparison of cultivar groups differing in end use showed that the genetic diversity of malting cultivars was significantly lower than that of feed cultivars, although modern malting and feed cultivars of Czechia and Slovakia have virtually the same genetic basis. Temporal analysis showed that diversity tended to increase through decades. While new original ancestors were introduced in pedigrees, especially in the past 30 years, the number of local landraces and old cultivars gradually decreased. The losses accounted for about two-thirds of the local germplasm. Thus, a substantial increase in genetic diversity was accompanied by genetic erosion of the local spring barley gene pool of former Czechoslovakia. A cluster structure was observed for the set of spring barley cultivars released in the postwar period. The coefficient of parentage averaged over all possible pairs of cultivars introduced in the Czech National List was estimated at 0.11. It was concluded that the genetic diversity of modern spring barley cultivars in the Czech Republic is at an acceptable level.     

Genetic diversity among barley cultivars assessed by sequence-specific amplification polymorphism

We analyzed the genetic structure and relationships among barley cultivars (Hordeum vulgare L.) with sequence-specific amplification polymorphisms (S-SAPs). Polymorphisms were identified in 824 individual barley plants representing 103 cultivars (eight plants per cultivar) widely grown in Canada and the United States, using PCR primers designed from the long terminal repeat of the barley retrotransposon BARE-1 and a subset of four selective MseI primers. From the 404 bands scored, 150 were polymorphic either within or between cultivars. Genetic structure assessed with analysis of molecular variance attributed the largest component of variation to the within groups of cultivars (69–86%). Within-cultivar genetic variation was estimated as average gene diversity over loci and ranged from 0 (completely homogenous) to 0.076 (most heterogeneous cultivar). Only 17 out of 103 cultivars (16%) were judged to be homogenous by this criterion. Relationships among cultivars were analyzed by cluster analysis using unweighted pair-groups using arithmetic averages and found groups similar to those determined by agriculturally significant phenotypic traits such as spike morphology (two-rowed or six-rowed), cultivar type (malting or feed), seed characteristic (hull-less or hulled), and growth habit (winter or spring), with minor overlaps. Discriminant analysis of groups determined by these phenotypic traits fully supported the different groups with minor overlaps between the malting/feed. S-SAP markers generated from retrotransposons such as BARE-1 are invaluable tools for the study of genetic diversity in organisms with a narrow genetic base such as barley. In this study, S-SAP analysis revealed significant amounts of cryptic variation in closely related cultivars including somaclonal variation, which could not be inferred by the pedigree analysis.     

Genotypic and phenotypic characterization of genetic differentiation and diversity in the USDA rice mini-core collection

A rice mini-core collection consisting of 217 accessions has been developed to represent the USDA core and whole collections that include 1,794 and 18,709 accessions, respectively. To improve the efficiency of mining valuable genes and broadening the genetic diversity in breeding, genetic structure and diversity were analyzed using both genotypic (128 molecular markers) and phenotypic (14 numerical traits) data. This mini-core had 13.5 alleles per locus, which is the most among the reported germplasm collections of rice. Similarly, polymorphic information content (PIC) value was 0.71 in the mini-core which is the highest with one exception. The high genetic diversity in the mini-core suggests there is a good possibility of mining genes of interest and selecting parents which will improve food production and quality. A model-based clustering analysis resulted in lowland rice including three groups, aus (39 accessions), indica (71) and their admixtures (5), upland rice including temperate japonica (32), tropical japonica (40), aromatic (6) and their admixtures (12) and wild rice (12) including glaberrima and four other species of Oryza. Group differentiation was analyzed using both genotypic distance Fst from 128 molecular markers and phenotypic (Mahalanobis) distance D(2) from 14 traits. Both dendrograms built by Fst and D(2) reached similar-differentiative relationship among these genetic groups, and the correlation coefficient showed high value 0.85 between Fst matrix and D(2) matrix. The information of genetic and phenotypic differentiation could be helpful for the association mapping of genes of interest. Analysis of genotypic and phenotypic diversity based on genetic structure would facilitate parent selection for broadening genetic base of modern rice cultivars via breeding effort.     

Inter-simple sequence repeat (ISSR) amplification for analysis of microsatellite motif frequency and fingerprinting in rice (Oryza sativa L.)

 Inter-simple sequence repeat (ISSR) amplification was used to analyze microsatellite motif frequency in the rice genome and to evaluate genetic diversity among rice cultivars. A total of 32 primers, containing different simple sequence repeat (SSR) motifs, were tested for amplification on a panel of 59 varieties, representative of the diversity of cultivated rice (Oryza sativa L.). The ISSR analysis provided insights into the organization, frequency and levels of polymorphism of different simple sequence repeats in rice. The more common dinucleotide motifs were more amenable to ISSR analysis than the more infrequent tri-, tetra- and penta-nucleotide motifs. The ISSR results suggested that within the dinucleotide class, the poly(GA) motif was more common than the poly(GT) motif and that the frequency and clustering of specific tri- and tetra-nucleotide simple sequence repeats was variable and motif-specific. Furthermore, trinucleotide ISSR markers were found to be less polymorphic than either dinucleotide or certain tetranucleotide ISSR markers, suggesting which motifs would be better targets for microsatellite marker development. The ISSR amplification pattern was used to group the rice genotypes by cluster analysis. These results were compared to surveys of the same varieties for amplified fragment length polymorphism (AFLP), restriction fragment length polymorphism (RFLP) and isozyme markers. The ISSR fingerprint could be used to differentiate the genotypes belonging to either Japonica or Indica sub species of cultivated rice and to dissect finer levels of diversity within each subspecies. A higher percentage of polymorphic bands was produced with the ISSR technique than the AFLP method, based on a similar PCR reaction. Therefore, ISSR amplification proved to be a valuable method for determining genetic variability among rice varieties and for rapidly identifying cultivars. This efficient genetic fingerprinting technique would be useful for characterizing the large numbers of rice accessions held in national and international germplasm centers. Received: 25 May 1998 / Accepted: 17 September 1998     

Genealogical analysis of the diversity of spring barley cultivars released in former Czechoslovakia and modern Czechia

Genealogical analysis was employed in studying the time course of changes in genetic diversity of spring barley cultivars released in former Czechoslovakia and the modem Czech Republic. Cultivars from different regions proved to significantly differ in the distribution of dominant ancestor contributions, suggesting a specificity of original ancestors to different cultivation conditions. A comparison of cultivar groups differing in end use showed that the genetic diversity of malting cultivars was significantly lower than that of feed cultivars, although modern malting and feed cultivars of Czechia and Slovakia have virtually the same genetic basis. Temporal analysis showed that diversity tended to increase through decades. While new original ancestors were introduced in pedigrees, especially in the past 30 years, the number of local landraces and old cultivars gradually decreased. The losses accounted for about two-thirds of the local germplasm. Thus, a substantial increase in genetic diversity was accompanied by genetic erosion of the local spring barley gene pool of former Czechoslovakia. A cluster structure was observed for the set of spring barley cultivars released in the postwar period. The coefficient of parentage averaged overall possible pairs of cultivars introduced in the Czech National List was estimated at 0.11. It was concluded that the genetic diversity of modern spring barley cultivars in the Czech Republic is at an acceptable level.     

A global barley panel revealing genomic signatures of breeding in modern Australian cultivars

The future of plant cultivar improvement lies in the evaluation of genetic resources from currently available germplasm. Today’s gene pool of crop genetic diversity has been shaped during domestication and more recently by breeding. Recent efforts in plant breeding have been aimed at developing new and improved varieties from poorly adapted crops to suit local environments. However, the impact of these breeding efforts is poorly understood. Here, we assess the contributions of both historical and recent breeding efforts to local adaptation and crop improvement in a global barley panel by analysing the distribution of genetic variants with respect to geographic region or historical breeding category. By tracing the impact that breeding had on the genetic diversity of Hordeum vulgare (barley) released in Australia, where the history of barley production is relatively young, we identify 69 candidate regions within 922 genes that were under selection pressure. We also show that modern Australian barley varieties exhibit 12% higher genetic diversity than historical cultivars. Finally, field-trialling and phenotyping for agriculturally relevant traits across a diverse range of Australian environments suggests that genomic regions under strong breeding selection and their candidate genes are closely associated with key agronomic traits. In conclusion, our combined data set and germplasm collection provide a rich source of genetic diversity that can be applied to understanding and improving environmental adaptation and enhanced yields.     

Local genetic structure in the critically endangered,cave‐associated perennial herb Primulina tabacum (Gesneriaceae)

The local spatial genetic structures of cave‐associated plants are seldom studied. Given that these plants are mainly confined to small areas in and around the entrances of caves, we hypothesized that they might lack genetic structures at local scales. To test this hypothesis, we sampled two large populations (named D and T) of a critically endangered perennial herb, Primulina tabacum, which is endemic to karst caves in southern China. We analysed nine microsatellite loci and sequenced four chloroplast DNA (cpDNA) intergenic spacer regions to study the genetic diversity and structure within and between both populations. Both populations have distinct genetic characteristics. Samples from two subpopulations in population D showed considerable genetic divergence. This is not consistent with the hypothesis that P. tabacum has a weak genetic structure at a local scale. However, 94% of the individuals in population T shared the same multilocus genotype, which indicates little genetic structure within this population. The contributions of seed flow, pollen flow and (sub)population history to the genetic diversity and structure in each and both populations are discussed. Our study is the first to investigate local genetic diversity and structure in a cave‐associated plant, and provides valuable information for the sustainable conservation of such species. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109 , 747–756.     

水稻轮回选择群体XTBG-HP1表型遗传多样性分析

该研究基于4个陆稻群体及172个水稻品种或杂交组合,构建了水稻多亲本隐性核不育轮回选择群体XTBG-HP1,并经过4次轮回重组,采用16个表型性状对其进行了遗传多样性分析。结果表明:(1)该群体14个数量性状符合正态分布,各表型均存在极端性状个体。(2)数量性状变异系数范围为0.08～0.41,均值为0.20; Shannon-Wiener多样性指数范围为0.72～1.92,均值为1.50。(3)群体在株型与产量构成因子性状方面有显著的相关性,对株型的选择可以实现产量性状的改良。(4)剑叶长、每穗粒总数、千粒重、穗长、粒长、一次枝梗数、有效穗数、剑叶宽、二次枝梗数、抽穗期10个性状可作为群体综合评价指标。(5)剑叶长、二次枝梗数、每穗粒总数3个表型性状具有较高的遗传变异、丰富的遗传多样性及与综合得分F值相关系数较高。综合以上结果发现,后期群体进行基因挖掘、品种改良以及优良育种材料的选育可以基于剑叶长、二次枝梗数及每穗粒总数3个表型性状,同时要充分利用群体株型与产量构成因子性状间的显著相关性。此外,该研究群体中极端单性状或综合得分F值较高的个体,可进一步用于品种选育。     

Natural and human‐mediated selection in a landrace of Thai rice (Oryza sativa)

Landrace rice in Thailand consists of managed populations grown under traditional and long‐standing agricultural practices. These populations evolve both in response to environmental conditions within the local agro‐ecosystem and in response to human activities. Single landraces are grown across varying environments and recently have experienced temporal changes in local environments due to climate change. Here we assess the interplay between natural selection in a changing climate and human‐mediated selection on the population genetic structure of Muey Nawng, a local landrace of Thai rice. Genetic diversity and population structure of landrace rice were assessed by a STRUCTURE analysis of 20 microsatellite loci. The first exon–intron junction of the waxy gene was sequenced to determine genotypes for glutinous or non‐glutinous grain starch. Muey Nawng rice is genetically variable and is structured based on starch grain types and the level of resistance to gall midge pest. A strong positive correlation was found between genetic diversity and the percentage of gall midge infestation. Variation in the waxy locus is correlated with starch quality; selection for non‐glutinous rice appears to involve additional genes. The dynamics of genetic diversity within Muey Nawng rice depends on three factors: (a) a genetic bottleneck caused by strong selection associated with gall midge infestation, (b) selection by local farmers for starch quality and (c) variation introduced by farmer practices for cultivation and seed exchange. These results, when taken in total, document the ability of landrace rice to quickly evolve in response to both natural and human‐mediated selection.     

Genetic diversity among Japanese indigenous common buckwheat (Fagopyrum esculentum) cultivars as determined from amplified fragment length polymorphism and simple sequence repeat markers and quantitative agronomic traits.

We assessed the genetic diversity in Japanese indigenous common buckwheat (Fagopyrum esculentum) cultivars using amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers and investigated the relationships between the genetic diversity and agronomic traits. The average expected intracultivar hetero zygosity was 0.303 for AFLP and 0.819 for SSR. The differentiations among agroecotypes, among cultivars within an agroecotype, and among cultivars were small (0.002, 0.024, and 0.026 for SSR and 0.013, 0.013, and 0.026 for AFLP, respectively) but statistically significant from zero except for the SSR differentiation among agroecotypes. In principal coordinates analysis, cultivars within the same agroecotype tended to cluster, indicating that agroecotypes well reflected the genetic relationships among cultivars. In AFLP, the differentiation among the agroecotypes was more distinct than in SSR, and genetic distance showed a moderate correlation with the difference in quantitative traits, indicating that AFLP can resolve the relationships among cultivars with better resolution than SSR. By contrast, SSR may be more sensitive to demographic changes. Four of the five SSR markers showed a significant positive correlation (Kendall's tau = 0.382-0.607) between allelic richness and variation in flowering timing, indicating that cumulative bottleneck events have occurred during the population history, with a decline in the variation of photosensitivity of flowering.