Genetic structure and isolation by distance in a landrace of Thai rice

Wild grapes of Armenia: unexplored source of genetic diversity and disease resistance

The present study is the first in-depth research evaluating the genetic diversity and potential resistance of Armenian wild grapes utilizing DNA-based markers to understand the genetic signature of this unexplored germplasm. In the proposed research, five geographical regions with known viticultural history were explored. A total of 148 unique wild genotypes were collected and included in the study with 48 wild individuals previously collected as seed. A total of 24 nSSR markers were utilized to establish a fingerprint database to infer information on the population genetic diversity and structure. Three nSSR markers linked to the Ren1 locus were analyzed to identify potential resistance against powdery mildew. According to molecular fingerprinting data, the Armenian V. sylvestris gene pool conserves a high genetic diversity, displaying 292 different alleles with 12.167 allele per loci. The clustering analyses and diversity parameters supported eight genetic groups with 5.6% admixed proportion. The study of genetic polymorphism at the Ren1 locus revealed that 28 wild genotypes carried three R-alleles and 34 wild genotypes carried two R-alleles associated with PM resistance among analyzed 107 wild individuals. This gene pool richness represents an immense reservoir of under-explored genetic diversity and breeding potential. Therefore, continued survey and research efforts are crucial for the conservation, sustainable management, and utilization of Armenian wild grape resources in the face of emerging challenges in viticulture.

Impact of Seed Origin and Genetic Drift of Improved Rice Variety IR841 in Benin

BACKGROUND

Rice production is important for food security in Benin, with a national production largely dominated by the cultivation of the aromatic ecotype IR841, by far the most appreciated by Beninese consumers. However, to maintain agronomical qualities of a given cultivar, the origin and quality of seeds are mandatory and at the heart of the maintenance of yield and of market requests. Following this idea, the objective of the current study was thus to investigate the genetic purity of IR841 varieties collected from rice producers across 22 villages in Benin in relation to their agronomical performances.

RESULTS

For this, agromorphological evaluation of 72 accessions based on 13 quantitative descriptors followed by genotyping with the Illumina Infinium rice 7 K SNP array of 9 accessions was carried out in the presence of 2 controls. Agromorphologic as well as genetic and phylogenetic analyses revealed two groups, the first one Okouta97, Koum47, Nana30, Man118, Ang1 and control sample IR841-2) was characterized by seed accessions provided by the formal seed system, while the second (Koum53, Tchaka41 and Koud46) comprising seeds from local markets or from previous harvests and showing a depression in agronomic performances.

CONCLUSION

We showed that IR841 seed purity is mandatory for the completion of agronomical performance, and that the farmers' choice of seeds must be guided and informed to ensure sustainability and food security.

Evaluation of Morpho-Physiological and Yield-Associated Traits of Rice (Oryza sativa L.) Landraces Combined with Marker-Assisted Selection under High-Temperature Stress and Elevated Atmospheric CO2 Levels

Rice (Oryza sativa L.) is an important cereal crop worldwide due to its long domestication history. North-Eastern India (NEI) is one of the origins of indica rice and contains various native landraces that can withstand climatic changes. The present study compared NEI rice landraces to a check variety for phenological, morpho-physiological, and yield-associated traits under high temperatures (HTs) and elevated CO2 (eCO2) levels using molecular markers. The first experiment tested 75 rice landraces for HT tolerance. Seven better-performing landraces and the check variety (N22) were evaluated for the above traits in bioreactors for two years (2019 and 2020) under control (T1) and two stress treatments [mild stress or T2 (eCO2 550 ppm + 4 °C more than ambient temperature) and severe stress or T3 (eCO2 750 ppm + 6 °C more than ambient temperature)]. The findings showed that moderate stress (T2) improved plant height (PH), leaf number (LN), leaf area (LA), spikelets panicle-1 (S/P), thousand-grain weight (TGW), harvest index (HI), and grain production. HT and eCO2 in T3 significantly decreased all genotypes' metrics, including grain yield (GY). Pollen traits are strongly and positively associated with spikelet fertility at maturity and GY under stress conditions. Shoot biomass positively affected yield-associated traits including S/P, TGW, HI, and GY. This study recorded an average reduction of 8.09% GY across two seasons in response to the conditions simulated in T3. Overall, two landraces-Kohima special and Lisem-were found to be more responsive compared to other the landraces as well as N22 under stress conditions, with a higher yield and biomass increment. SCoT-marker-assisted genotyping amplified 77 alleles, 55 of which were polymorphic, with polymorphism information content (PIC) values from 0.22 to 0.67. The study reveals genetic variation among the rice lines and supports Kohima Special and Lisem's close relationship. These two better-performing rice landraces are useful pre-breeding resources for future rice-breeding programs to increase stress tolerance, especially to HT and high eCO2 levels under changing climatic situations.

Screening of Ginkgo Individuals with Superior Growth Structural Characteristics in Different Genetic Groups Using Terrestrial Laser Scanning (TLS) Data

With the concept of sustainable management of plantations, individual trees with excellent characteristics in plantations have received attention from breeders. To improve and maintain long-term productivity, accurate and high-throughput access to phenotypic characteristics is essential when establishing breeding strategies. Meanwhile, genetic diversity is also an important issue that must be considered, especially for plantations without seed source information. This study was carried out in a ginkgo timber plantation. We used simple sequence repeat (SSR) markers for genetic background analysis and high-density terrestrial laser scanning for growth structural characteristic extraction, aiming to provide a possibility of applying remote sensing approaches for forest breeding. First, we analyzed the genetic diversity and population structure, and grouped individual trees according to the genetic distance. Then, the growth structural characteristics (height, diameter at breast height, crown width, crown area, crown volume, height to living crown, trunk volume, biomass of all components) were extracted. Finally, individual trees in each group were comprehensively evaluated and the best-performing ones were selected. Results illustrate that terrestrial laser scanning (TLS) point cloud data can provide nondestructive estimates of the growth structural characteristics at fine scale. From the ginkgo plantation containing high genetic diversity (average polymorphism information content index was 0.719) and high variation in growth structural characteristics (coefficient of variation ranged from 21.822% to 85.477%), 11 excellent individual trees with superior growth were determined. Our study guides the scientific management of plantations and also provides a potential for applying remote sensing technologies to accelerate forest breeding.

Genetic Diversity and Population Structure of Common Bean (Phaseolus vulgaris L.) Landraces in the Lazio Region of Italy

Common bean cultivation has historically been a typical component of rural economies in Italy, particularly in mountainous and hilly zones along the Apennine ridge of the central and southern regions, where the production is focused on local landraces cultivated by small-scale farmers using low-input production systems. Such landraces are at risk of genetic erosion because of the recent socioeconomic changes in rural communities. One hundred fourteen accessions belonging to 66 landraces still being grown in the Lazio region were characterized using a multidisciplinary approach. This approach included morphological (seed traits), biochemical (phaseolin and phytohemagglutinin patterns), and molecular (microsatellite loci) analyses to investigate their genetic variation, structure, and distinctiveness, which will be essential for the implementation of adequate ex situ and in situ conservation strategies. Another objective of this study was to determine the original gene pool (Andean and Mesoamerican) of the investigated landraces and to evaluate the cross-hybridization events between the two ancestral gene pools in the P. vulgaris germplasm in the Lazio region. Molecular analyses on 456 samples (four for each of the 114 accessions) revealed that the P. vulgaris germplasm in the Lazio region exhibited a high level of genetic diversity (He = 0.622) and that the Mesoamerican and Andean gene pools were clearly differentiated, with the Andean gene pool prevailing (77%) and 12% of landraces representing putative hybrids between the two gene pools. A model-based cluster analysis based on the molecular markers highlighted three main groups in agreement with the phaseolin patterns and growth habit of landraces. The combined utilisation of morphological, biochemical, and molecular data allowed for the differentiation of all landraces and the resolution of certain instances of homonymy and synonymy. Furthermore, although a high level of homozygosity was found across all landraces, 32 of the 66 examined (49%) exhibited genetic variability, indicating that the analysis based on a single or few plants per landrace, as usually carried out, may provide incomplete information.

Harnessing intra-varietal variation for agro-morphological and nutritional traits in a popular rice landrace for sustainable food security in tropical islands

Introduction

Rice crop meets the calorie and nutritional requirements of a larger segment of the global population. Here, we report the occurrence of intra-varietal variation in a popular rice landrace C14-8 traditionally grown under the geographical isolation of the Andaman Islands.

Methods

Based on grain husk color, four groups were formed, wherein the extent of intra-varietal variation was studied by employing 22 agro-morphological and biochemical traits.

Results

Among the traits studied, flavonoid and anthocyanin contents and grain yield exhibited a wider spectrum of variability due to more coefficients of variation (>25%). The first five principal components (PCs) of principal components analysis explained a significant proportion of the variation (91%) and the first two PCs explained 63.3% of the total variation, with PC1 and PC2 explaining 35.44 and 27.91%, respectively. A total of 50 highly variable SSR (HvSSR) markers spanning over 12 chromosomes produced 314 alleles, which ranged from 1 to 15 alleles per marker, with an average of 6.28. Of the 314 alleles, 64 alleles were found to be rare among the C14-8 selections. While 62% of HvSSR markers exhibited polymorphism among the C14-8 population, chromosomes 2, 7, 9, and 11 harbored the most polymorphic loci. The group clustering of the selections through HvSSR markers conformed to the grouping based on grain husk coloration.

Discussion

Our studies on the existence and pertinence of intra-varietal variations are expected to be of significance in the realms of evolutionary biology and sustainable food and nutritional security under the changing climate.

Morpho-physiological, biochemical and molecular characterization of coastal rice landraces to identify novel genetic sources of salinity tolerance

Soil salinity is a leading cause for yield losses in rice, affecting nearly 6% of global rice cultivable area. India is host to a rich diversity of coastal rice landraces that are naturally tolerant to salinity and an untapped source to identify novel determinants of salinity tolerance. In the present study, we have assessed the relative salinity tolerance of 43 previously genotyped rice landraces at seedling stage, using thirteen morpho-physiological and biochemical parameters using a hydroponics system. Among 43 rice varieties, 25 were tolerant, 15 were moderately tolerant, 1 was moderately susceptible and 2 sensitive checks were found to be highly susceptible based on standard salinity scoring methods. In addition to previously known saline tolerant genotypes (Pokkali, FL478 and Nona Bokra), the present study has novel genotypes such as Katrangi, Orkyma, Aduisen 1, Orumundakan 1, Hoogla, and Talmugur 2 as potential sources of salinity tolerance through measurement of morpho-physiological and biochemical parameters including Na+, K+ estimations and Na+/K+ ratios. Further, Pallipuram Pokkali may be an important source of the tissue tolerance trait under salinity. Four marker trait associations (RM455-root Na+; RM161-shoot and root Na+/K+ ratios; RM237-salinity tolerance index) accounted for phenotypic variations in the range of 20.97-39.82%. A significant increase in root endodermal and exodermal suberization was observed in selected rice landraces under salinity. For the first time, variation in the number of suberized sclerenchymatous layers as well as passage cells is reported, in addition to expression level changes in suberin biosynthetic genes (CYP86A2, CYP81B1, CYP86A8 and PERL).

Extensive Sampling Provides New Insights into Phylogenetic Relationships between Wild and Domesticated Zanthoxylum Species in China

Zanthoxylum, belonging to the Rutaceae family, is widely distributed in tropical and subtropical regions. The genus has high economic value as spices, oils, medicinal plants, and culinary applications. Zanthoxylum has a long history of domestication and cultivation in China. However, the phylogenetic relationships and origin of wild and cultivated Zanthoxylum species in China remain largely unknown. Moreover, there is still no clear molecular phylogenetic system for Zanthoxylum species. Herein, 373 Zanthoxylum samples were collected from all presently known provenances of Zanthoxylum in China. In this study, four chloroplast DNA (cpDNA) markers (matK, ndhH, psbB, rbcL) were used to comprehensively analyze the genetic diversity, relatedness, and geographical origin of Chinese Zanthoxylum species. The results were as follows: (1) The aligned length of the four pairs of cpDNA sequences was 3836 bp, and 68 haplotypes were identified according to 219 variable polymorphic sites, including 3 Indels (insertions and deletions), 129 parsimony informative sites, 90 singleton variable sites. (2) Phylogenetic tree and haplotype network strongly supported the division of Zanthoxylum species consistent with the taxonomic recognition of five species: Z. bungeanum, Z. piasezkii, Z. piperitum, Z. armatum, and Z. micranthum. (3) Divergence time estimation suggested that Zanthoxylum genus originated from the Late Eocene, and most Zanthoxylum species diverged after the Middle Miocene. (4) Haplotype 16 (H16) was at the bottom of the phylogenetic tree, had higher haplotype diversity (Hd) and nucleotide polymorphism (Pi) than other haplotypes, and was located in the center of the network figure. Therefore, we deduced that the cultivated Zanthoxylum species may originate in Zhouqu County, Gansu Province, China. Meanwhile, our research provided a scientific basis for the identification and breeding programs of Chinese Zanthoxylum species.

Whole Genome Resequencing of 20 Accessions of Rice Landraces Reveals Javanica Genomic Structure Variation and Allelic Genotypes of a Grain Weight Gene TGW2

The landraces preserved by indigenous worldwide exhibited larger variation in the phenotypes and adaption to different environments, which suggests that they comprise rich resources and can be served as a gene pool for rice improvement. Despite extensive studies on cultivated rice, the variations and relationships between landraces and modern cultivated rice remain unclear. In this study, a total of 20 varieties that include 10 Oryza javanica collected from different countries worldwide and 10 Oryza indica from China were genotyped and yielded a sum of 99.9-Gb resequencing raw data. With the genomic sequence of the japonica cultivar Nipponbare as a reference, the following genetic features of single-nucleotide polymorphism (SNP) ranged from 861,177 to 1,044,617, insertion-deletion polymorphisms (InDels) ranged from 164,018 to 211,135, and structural variation (SV) ranged from 3,313 to 4,959 were identified in Oryza javanica. Variation between the two subspecies was also determined that 584,104 SNPs, 75,351 InDels, 104,606 SNPs, and 19,872 InDels specific to Oryza indica and Oryza javanica, respectively. Furthermore, Gene Ontology (GO) and KEGG of Oryza javanica-specific SNP-related genes revealed that they participated in DNA metabolic process, DNA replication, and DNA integration. The sequence variation and candidate grain shape-related gene TGW2 were identified through Fst and sweep selective analysis. Hap4 of TGW2 is performed better than others. The whole genome sequence data and genetic variation information illustrated in this study will serve as an important gene pool for molecular breeding and facilitate genetic analysis of Oryza javanica varieties.

Genetic Diversity and Environmental Influence on Yield and Yield-Related Traits of Adzuki Bean (Vigna angularis L.)

Adzuki beans are an important food legume crop in East Asia. A large number of adzuki bean accessions are maintained in the Chinese national seed genebank. A collection of 59 elite cultivars, 389 landraces, and 27 wild adzuki beans were selected and phenotyped extensively for yield and yield-related traits at two different locations (Nanning and Nanyang, China). Ten agronomic and yield-related traits were scored, and the data were subjected to analysis of variance (ANOVA), principal component analysis (PCA), correlation, and cluster analysis. Significant variation was observed for genotypes, locations, and genotype x environment interaction for most traits. Also, there were significant differences in the phenotypes among accessions of different germplasm types. The broad-sense heritability of traits studied ranged from 4.4% to 77.8%. The number of seeds per pod (77.8%), 100-seed weight (68.0%), and number of plant branches (63.9%) had a high heritability. A total of 10 traits were transformed into 3 comprehensive factors by principal component analysis, and the first three principal component factors contributed 72.31% of the total variability. Cluster analysis categorized the 475 adzuki bean accessions into five distinct groups. The results described in this study will be useful for adzuki bean breeders for the development of varieties with high end-use quality.

Traditional agricultural management of Kam Sweet Rice (Oryza sativa L.) in southeast Guizhou Province, China

BACKGROUND

The Dong people mainly live in Hunan, Guangxi and Guizhou provinces, China, with a long history of glutinous rice cultivation, among which Kam Sweet Rice (KSR) is a group of rice landraces that has been domesticated for thousands of years by the Dong people. The core distribution area of KSR is Liping, Congjiang and Rongjiang County of southeast, Guizhou Province. Paddy fields, forests, livestock and cottages have formed a special artificial wetland ecosystem in local area, and the Dong people have also formed a set of traditional farming systems of KSR for variety breeding, field management, and soil and water conservation. However, this traditional agricultural management has not been reported at multiple levels based on landraces, species and ecosystems.

METHODS

Fieldwork was conducted in ten villages in southeast Guizhou from 2019 to 2021. A total of 229 informants were interviewed from the villages. Semi-structured and key informant interviews were administered to collect ethnoecological data on the characteristics and traditional utilization of KSR, traditional farming systems and agricultural management of the Dong people.

RESULTS

(1): A total of 57 KSR landraces were recorded as used by the Dong people in southeast Guizhou. We analyzed the cultural importance index (CII) of all KSRs. KSR with high CII often has a pleasant taste, special biological characteristics of cold resistance, disease and insect resistance and high utilization in the traditional culture of Dong people. (2) There is a clear division of labor between men and women in the breeding, seed retention, field management and grain storage management of different landraces of KSR in Dong communities. In order to resist natural disasters and insect pests, the cultivation of KSR is usually managed by multi-variety mixed planting. These agricultural management modes are the result of Dong people's understanding and adaptation to the local natural geographical environment, as well as the experience and wisdom crystallization of Dong people's long-term practice. (3) The traditional farmland of Dong People is a typical artificial wetland ecosystem that is planted with mixed KSR landraces with rich traditional wisdom. In addition, the economic benefit of the rice-fish-duck symbiotic system was 3.07 times that of hybrid rice alone; therefore, the rice-fish-duck system not only has the function of maintaining soil, water and ecological balance but also improves the income of Dong people.

CONCLUSION

KSR is a special kind of rice that has been domesticated and cultivated by Dong people for thousands of years. Dong people have also formed traditional agriculture dominated by KSR cultivation. The traditional agricultural management of Dong people provides suitable habitats for flora and fauna with biodiversity protection, and convenient conditions for rational utilization and distribution of water resources were also provided. This traditional management mode is of great significance for environmental protection, climate change response, community resource management, sustainable utilization and agricultural transformation in modern society. Therefore, we call for interdisciplinary research in natural and social sciences, in-depth study of the ecological culture of ethnic areas, and sort out treasures conducive to the development of all mankind.

Kam Sweet Rice (Oryza sativa L.) Is a Special Ecotypic Rice in Southeast Guizhou, China as Revealed by Genetic Diversity Analysis

Kam Sweet Rice (KSR) is a special kind of rice landrace that has been domesticated for thousands of years by the local Dong people in southeast Guizhou province, China. KSR has many distinguishing characteristics including strong fragrance; high resistance to diseases, pests, and adverse abiotic conditions; difficulty of threshing; and glutinous texture. There is a lack of systematic research on its genetic diversity. In this study, we analyzed the levels and patterns of genetic diversity and nucleotide variation in 1,481 rice germplasm using simple sequence repeat (SSR) markers and single nucleotide polymorphism (SNP) haplotype analysis of six unlinked nuclear loci. The accessions included 315 KSR resources from southeast Guizhou, 578 rice landraces from six rice-growing ecological zones in Guizhou, 546 rice landraces from nine provinces around Guizhou, and 42 wild rice sources. Genetic diversity and heterozygosity of KSR were both low, and thus KSR might be close to a pure rice line. Population structure analysis showed that KSR was isolated into a single type of rice, which had a large genetic distance and a unique genetic background compared to the local varieties in Guizhou province, indicating that KSR is a special rice ecotype. Haplotype analysis of the target genes showed that the population of KSR was rich in haplotypes for resistance to bacterial blight (Xa23) and rice blast (Pid3), and identified unique haplotypes that were different from those of the six rice ecotypes in Guizhou. This study shows that KSR is an excellent rice germplasm resource, provides important information for the improvement and utilization of rice landraces, and serves as a reference for formulating effective rice conservation measures.

Characterization and exploring genetic potential of landraces from Odisha with special emphasis on grain micronutrient content for benefaction of biofortification in rice

Assessing genetic variability of micronutrient content in association with qualitative and quantitative traits in germplasm is prerequisite for effective biofortification programme. Odisha, a state of eastern India is considered as one of the most potential hot spot of diversity of cultivated rice for grain yield and nutritional traits. Significant variability for most of the qualitative and quantitative traits including Fe and Zn content was observed in a set of 293 germplasm with varying kernel colour encompassing 14 districts of Odisha. Mostly these landraces were low yielding with some exception (Haldigundi: AC 36454, 50.08 g/plant). These landraces were mostly represented by medium Fe (10-20 ppm)-medium Zn group (20-30 ppm). Fe and Zn content had positive association with each other and also with grain size. Landraces with red kernel colour were observed to have slightly higher average Zn content (26.30 ppm) as compared to white (25.87 ppm) grains. Diversity analysis of 14 districts revealed that Nayagarh, a south-eastern district was rich in Fe content while Deogarh, Keonjhar and Mayurbhanj, all north-western districts were rich in Zn content. This study identified 10 superior micronutrient dense genotypes with medium to high Fe and Zn content. This set of donors for micronutrient content was validated in another year. Champeisiali (AC 43368) and Gedemalati (AC 34306) with highest Fe (44.1 ppm) and Zn (40.48 ppm) content, respectively were detected over the environments. Identified donors and associated traits could be utilized in biofortificaion programme using appropriate breeding methodologies for enhancing micronutrients in high yielding background.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-01119-7.

NILs of Cold Tolerant Japonica Cultivar Exhibited New QTLs for Mineral Elements in Rice

Chilling stress at booting stage can cause floret deterioration and sterility by limiting the supply of food chain and the accumulation of essential mineral elements resulting in reduction of yield and grain quality attributes in rice. Genomic selection of chilling tolerant rice with reference to the accumulation of mineral elements will have great potential to cope with malnutrition and food security in times of climate change. Therefore, a study was conducted to explore the genomic determinants of cold tolerance and mineral elements content in near-isogenic lines (NILs) of japonica rice subjected to chilling stress at flowering stage. Detailed morphological analysis followed by quantitative analysis of 17 mineral elements revealed that the content of phosphorus (P, 3,253 mg/kg) and potassium (K, 2,485 mg/kg) were highest while strontium (Sr, 0.26 mg/kg) and boron (B, 0.34 mg/kg) were lowest among the mineral elements. The correlation analysis revealed extremely positive correlation of phosphorus (P) and copper (Cu) with most of the cold tolerance traits. Among all the effective ear and the second leaf length correlation was significant with half of the mineral elements. As a result of comparative analysis, some QTLs (qBRCC-1, qBRCIC-2, qBRZC-6, qBRCHC-6, qBRMC-6, qBRCIC-6a, qBRCIC-6b, qBRCHC-6, and qBRMC-6) identified for calcium (Ca), zinc (Zn), chromium (Cr) and magnesium (Mg) on chromosome number 1, 2, and 6 while, a novel QTL (qBCPC-1) was identified on chromosome number 1 for P element only. These findings provided bases for the identification of candidate genes involved in mineral accumulation and cold tolerance in rice at booting stage.

Genetic Structure and Geographical Differentiation of Traditional Rice (Oryza sativa L.) from Northern Vietnam

Northern Vietnam is one of the most important centers of genetic diversity for cultivated rice. Over thousands of years of cultivation, natural and artificial selection has preserved many traditional rice landraces in northern Vietnam due to its geographic situation, climatic conditions, and many ethnic groups. These local landraces serve as a rich source of genetic variation—an important resource for future crop improvement. In this study, we determined the genetic diversity and population structure of 79 rice landraces collected from northern Vietnam and 19 rice accessions collected from different countries. In total, 98 rice accessions could be differentiated into japonica and indica with moderate genetic diversity and a polymorphism information content of 0.382. Moreover, we found that genetic differentiation was related to geographical regions with an overall PhiPT (analog of fixation index F_ST) value of 0.130. We also detected subspecies-specific markers to classify rice (Oryza sativa L.) into indica and japonica. Additionally, we detected five marker-trait associations and rare alleles that can be applied in future breeding programs. Our results suggest that rice landraces in northern Vietnam have a dynamic genetic system that can create different levels of genetic differentiation among regions, but also maintain a balanced genetic diversity between regions.

Genetic differentiation and restricted gene flow in rice landraces from Yunnan, China: effects of isolation-by-distance and isolation-by-environment

BACKGROUND

Understanding and identifying the factors responsible for genetic differentiation is of fundamental importance for efficient utilization and conservation of traditional rice landraces. In this study, we examined the spatial genetic differentiation of 594 individuals sampled from 28 locations in Yunnan Province, China, covering a wide geographic distribution and diverse growing conditions. All 594 accessions were studied using ten unlinked target genes and 48 microsatellite loci, and the representative 108 accessions from the whole collection were sampled for resequencing.

RESULTS

The genetic diversity of rice landraces was quite different geographically and exhibited a geographical decline from south to north in Yunnan, China. Population structure revealed that the rice landraces could be clearly differentiated into japonica and indica groups, respectively. In each group, the rice accessions could be further differentiated corresponded to their geographic locations, including three subgroups from northern, southern and middle locations. We found more obvious internal geographic structure in the japonica group than in the indica group. In the japonica group, we found that genetic and phenotypic differentiation were strongly related to geographical distance, suggesting a pattern of isolation by distance (IBD); this relationship remained highly significant when we controlled for environmental effects, where the likelihood of gene flow is inversely proportional to the distance between locations. Moreover, the gene flow also followed patterns of isolation by environment (IBE) whereby gene flow rates are higher in similar environments. We detected 314 and 216 regions had been differentially selected between Jap-N and Jap-S, Ind-N and Ind-S, respectively, and thus referred to as selection signatures for different geographic subgroups. We also observed a number of significant and interesting associations between loci and environmental factors, which implies adaptation to local environment.

CONCLUSIONS

Our findings highlight the influence of geographical isolation and environmental heterogeneity on the pattern of the gene flow, and demonstrate that both geographical isolation and environment drives adaptive divergence play dominant roles in the genetic differentiation of the rice landraces in Yunnan, China as a result of limited dispersal.

Genetic Diversity of Landraces and Improved Varieties of Rice (Oryza sativa L.) in Taiwan

BACKGROUND

Rice, the most important crop in Asia, has been cultivated in Taiwan for more than 5000 years. The landraces preserved by indigenous peoples and brought by immigrants from China hundreds of years ago exhibit large variation in morphology, implying that they comprise rich genetic resources. Breeding goals according to the preferences of farmers, consumers and government policies also alter gene pools and genetic diversity of improved varieties. To unveil how genetic diversity is affected by natural, farmers', and breeders' selections is crucial for germplasm conservation and crop improvement.

RESULTS

A diversity panel of 148 rice accessions, including 47 cultivars and 59 landraces from Taiwan and 42 accessions from other countries, were genotyped by using 75 molecular markers that revealed an average of 12.7 alleles per locus with mean polymorphism information content of 0.72. These accessions could be grouped into five subpopulations corresponding to wild rice, japonica landraces, indica landraces, indica cultivars, and japonica cultivars. The genetic diversity within subpopulations was: wild rices > landraces > cultivars; and indica rice > japonica rice. Despite having less variation among cultivars, japonica landraces had greater genetic variation than indica landraces because the majority of Taiwanese japonica landraces preserved by indigenous peoples were classified as tropical japonica. Two major clusters of indica landraces were formed by phylogenetic analysis, in accordance with immigration from two origins. Genetic erosion had occurred in later japonica varieties due to a narrow selection of germplasm being incorporated into breeding programs for premium grain quality. Genetic differentiation between early and late cultivars was significant in japonica (F_ST = 0.3751) but not in indica (F_ST = 0.0045), indicating effects of different breeding goals on modern germplasm. Indigenous landraces with unique intermediate and admixed genetic backgrounds were untapped, representing valuable resources for rice breeding.

CONCLUSIONS

The genetic diversity of improved rice varieties has been substantially shaped by breeding goals, leading to differentiation between indica and japonica cultivars. Taiwanese landraces with different origins possess various and unique genetic backgrounds. Taiwanese rice germplasm provides diverse genetic variation for association mapping to unveil useful genes and is a precious genetic reservoir for rice improvement.

Adaptation to novel environments during crop diversification

In the context of the global challenge of climate change, mitigation strategies are needed to adapt crops to novel environments. The main goal to address this is an understanding of the genetic basis of crop adaptation to different agro-ecological conditions. The movement of crops during the Colombian Exchange that started with the travels of Columbus in 1492 is an example of rapid adaptation to novel environments. Many diversification-related traits have been characterised in multiple crop species, and association-mapping analyses have identified loci involved in these. Here, we present an overview of current knowledge regarding the molecular basis related to the complex patterns of crop adaptation and dissemination, particularly outside their centres of origin. Investigation of the genomic basis of crop expansion offers a powerful contribution to the development of tools to identify and exploit valuable genetic diversity and to improve and design novel resilient crop varieties.

Genetic Diversity and Evolutionary Relationships of Chinese Pepper Based on nrDNA Markers

Chinese pepper, referring to Zanthoxylum bungeanum Maxim. and Zanthoxylum armatum DC. species, is an important spice crop that has long attracted people’s interest due to its extensive application in Asian cuisine to improve taste. Numerous cultivars have been developed during the long history of domestication and cultivation. However, little to no information is available on the genetic diversity and evolutionary relationships of Chinese pepper cultivars and their historical diversification has not been clarified. Herein, we sequenced two nrDNA non-coding region markers, the external transcribed spacer (ETS) and the internal transcribed spacer 2 (ITS2), to assess genetic diversity and phylogenetic relationships among 39 cultivated and wild populations of Chinese pepper from eight provinces and to address the question of ancient demographic trends which were probably influenced by changing climate during evolutionary history. In total, 31 haplotypes were identified based on 101 polymorphism sites. Our results revealed relatively high level of genetic variation despite long-term cultivation of this crop. AMOVA revealed that genetic variation existed predominantly within provinces rather than among provinces. The genetic structure result based on haplotype network analysis largely reflected historical records, which suggested a Gansu origin for Chinese pepper and an ancient west-to-east spread of Chinese pepper circulating in China. We also provided evidence that changing Pleistocene climates had shaped the demographic trends of Chinese pepper. Taken together, our findings not only suggest that Chinese pepper is a dynamic genetic system that responds to evolutionary forces, but it also provides a fundamental genetic profile for the conservation and responsible exploitation of the extant germplasm of Chinese pepper and for improving the genetic basis for breeding the cultivars.

Genomic analyses reveal selection footprints in rice landraces grown under on-farm conservation conditions during a short-term period of domestication

Traditional rice landraces grown under on-farm conservation conditions by indigenous farmers are extremely important for future crop improvement. However, little is known about how the natural selection and agriculture practices of indigenous farmers interact to shape and change the population genetics of rice landraces grown under on-farm conservation conditions during the domestication. In this study, we sequenced DNA from 108 core on-farm conserved rice landraces collected from the ethnic minority regions of Yunnan, China, including 56 accessions collected in 1980 and 52 accessions collected in 2007 and obtained 2,771,245 of credible SNPs. Our findings show that most genetic diversity was retained during the 27 years of domestication by on-farm conservation. However, SNPs with marked allele frequency differences were found in some genome regions, particularly enriched in genic regions, indicating changes in genic regions may have played a much more prominent role in the short-term domestication of 27 years. We identified 186 and 183 potential selective-sweep regions in the indica and japonica genomes, respectively. We propose that on-farm conserved rice landraces during the short-term domestication had a highly polygenic basis with many loci responding to selection rather than a few loci with critical changes in response to selection. Moreover, loci affecting important agronomic traits and biotic or abiotic stress responses have been particularly targeted in selection. A genome-wide association study identified 90 significant signals for six traits, 13 of which were in regions of selective sweeps. Moreover, we observed a number of significant and interesting associations between loci and environmental factors, which implies adaptation to local environment. Our results provide insights into short-term evolutionary processes and shed light on the underlying mechanisms of on-farm conservation.

The maintenance of stable yield and high genetic diversity in the agricultural heritage torreya tree system

BACKGROUND

Understanding how traditional agriculture systems have been maintained would help design sustainable agriculture. In this study, we examined how farmers have used two types of local trees (Torreya grandis) for stable yield and maintaining genetic diversity in the "globally important agricultural heritage torreya tree system". The two type of torreya trees are grafted torreya (GT) tree and non-grafted-torreya (NGT) tree. The GT tree has only female and was used to produced seed yields. The NGT tree has both male and female and was used to support GT tree by providing pollens and rootstocks. We first tested the ratio of GT tree to NGT tree, their age groups, ratio of female trees (including GT and NGT trees) to male, and the flowering period of GT and NGT trees. We then tested seed yields and genetic diversity of GT and NGT trees. We further tested gene flow among NGT trees, and the relationship of gene flow with exchange rates of pollens and seeds.

RESULTS

GT and NGT trees (male and female) were planted in a mosaic pattern with a ratio of 4:1 (GT:NGT). In this planting pattern, one NGT male trees provided pollen for 20 female trees of GT and NGT. The trees were classified into four age groups (I = 100-400 years old; II = 400-700 years old; III = 700-1000 years old; and IV = 1000-1300 years old) based on basal diameter. The entire flowering period was longer for NGT trees than for GT trees that ensured GT trees (which lack of males) being exposed to pollens. GT tree had high and stable seed yield that increased with age groups. High genetic diversity has been maintained in both rootstocks of the GT trees and NGT trees. There was a strong gene flow among NGT trees, which positive correlated with the exchange rates of pollens and seeds.

CONCLUSIONS

Our results suggest that farmers obtain stable seed yields, and maintain high genetic diversity by ingeniously using the local GT tree as yield producer and NGT tree as supporter. These GT and NGT trees together ensure sustainable torreya production.

Modeling Epidemics in Seed Systems and Landscapes To Guide Management Strategies: The Case of Sweet Potato in Northern Uganda

Seed systems are critical for deployment of improved varieties but also can serve as major conduits for the spread of seedborne pathogens. As in many other epidemic systems, epidemic risk in seed systems often depends on the structure of networks of trade, social interactions, and landscape connectivity. In a case study, we evaluated the structure of an informal sweet potato seed system in the Gulu region of northern Uganda for its vulnerability to the spread of emerging epidemics and its utility for disseminating improved varieties. Seed transaction data were collected by surveying vine sellers weekly during the 2014 growing season. We combined data from these observed seed transactions with estimated dispersal risk based on village-to-village proximity to create a multilayer network or "supranetwork." Both the inverse power law function and negative exponential function, common models for dispersal kernels, were evaluated in a sensitivity analysis/uncertainty quantification across a range of parameters chosen to represent spread based on proximity in the landscape. In a set of simulation experiments, we modeled the introduction of a novel pathogen and evaluated the influence of spread parameters on the selection of villages for surveillance and management. We found that the starting position in the network was critical for epidemic progress and final epidemic outcomes, largely driven by node out-degree. The efficacy of node centrality measures was evaluated for utility in identifying villages in the network to manage and limit disease spread. Node degree often performed as well as other, more complicated centrality measures for the networks where village-to-village spread was modeled by the inverse power law, whereas betweenness centrality was often more effective for negative exponential dispersal. This analysis framework can be applied to provide recommendations for a wide variety of seed systems.[Formula: see text] Copyright © 2019 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Genetic Diversity and Population Structure in Upland Rice (Oryza sativa L.) of Mizoram, North East India as Revealed by Morphological, Biochemical and Molecular Markers

Upland rice landraces from different villages of Mizoram, Northeast India were analyzed for seed morphology, amylose content, aromatic characteristic, seed storage protein profiling and genetic diversity. Results revealed variation in grain length, width, weight and shape. Protein profiling showed polypeptide bands ranging from 7 to 10 with similarity coefficient from 0.556 to 1.000 in the studied populations. Population genetic analysis using simple sequence repeats markers revealed a total of 63 alleles with a high level of gene diversity at 0.6468. High values of Fst and PIC estimates were found at 0.7239 and 0.5984 respectively. The Biruchuk population was found to be the most genetically diverse cultivar and least gene diversity was found in Tuikuk buh. The UPGMA trees based on seed morphology, seed storage protein profiling and simple sequence repeats diversity showed the grouping of rice cultivars into three clusters which were further supported by model-based STRUCTURE analysis. This finding is the first-hand report in upland rice of the state and can be useful for selecting suitable rice lines for prebreeding and germplasm conservation of indigenous hill rice cultivars of Mizoram.

Morphological and Molecular Data Reveal Three Distinct Populations of Indian Wild Rice Oryza rufipogon Griff. Species Complex

Wild relatives of crops possess adaptive mutations for agronomically important traits, which could play significant role in crop improvement for sustainable agriculture. However, global climate change and human activities pose serious threats to the natural habitats leading to erosion of genetic diversity of wild rice populations. The purpose of this study was to explore and characterize India's huge untapped wild rice diversity in Oryza rufipogon Griff. species complex from a wide range of ecological niches. We made strategic expeditions around diversity hot spots in 64 districts of nine different agro-climatic zones of the country and collected 418 wild rice accessions. Significant variation was observed among the accessions for 46 morphological descriptors, allowing classification into O. nivara, O. rufipogon, and O. sativa f. spontanea morpho-taxonomic groups. Genome-specific pSINE1 markers confirmed all the accessions having AA genome, which were further classified using ecotype-specific pSINE1 markers into annual, perennial, intermediate, and an unknown type. Principal component analysis revealed continuous variation for the morphological traits in each ecotype group. Genetic diversity analysis based on multi-allelic SSR markers clustered these accessions into three major groups and analysis of molecular variance for nine agro-climatic zones showed that 68% of the genetic variation was inherent amongst individuals while only 11% of the variation separated the zones, though there was significant correlation between genetic and spatial distances of the accessions. Model based population structure analysis using genome wide bi-allelic SNP markers revealed three sub-populations designated 'Pro-Indica,' 'Pro-Aus,' and 'Mid-Gangetic,' which showed poor correspondence with the morpho-taxonomic classification or pSINE1 ecotypes. There was Pan-India distribution of the 'Pro-Indica' and 'Pro-Aus' sub-populations across agro-climatic zones, indicating a more fundamental grouping based on the ancestry closely related to 'Indica' and 'Aus' groups of rice cultivars. The Pro-Indica population has substantial presence in the Eastern Himalayan Region and Lower Gangetic Plains, whereas 'Pro-Aus' sub-population was predominant in the Upper Gangetic Plains, Western Himalayan Region, Gujarat Plains and Hills, and Western Coastal Plains. In contrast 'Mid-Gangetic' population was largely concentrated in the Mid Gangetic Plains. The information presented here will be useful in the utilization of wild rice resources for varietal improvement.

Preservation of the genetic diversity of a local common carp in the agricultural heritage rice-fish system

This paper contributes to understanding how traditional agriculture can maintain large genetic diversity. We quantify the effects of traditional farmer activities on the genetic diversity of an indigenous common carp in the 1,200-y-old agriculture heritage rice−fish system. We show that small farmer households interdependently incubating fish fry for their rice−fish farming shape the genetic pattern and help to maintain high genetic diversity of this local common carp. We also show how the traditional practice of mixed culturing of diverse color types potentially promotes genetic diversity. We suggest that the locally adapted ways of traditional farmers obtaining and using local genetic resources for their farming play an important role in the biodiversity of farmed crops and animals. It can become a “hotspot” for genetic diversity conservation in agriculture.

We examined how traditional farmers preserve the genetic diversity of a local common carp (Cyprinus carpio), which is locally referred to as “paddy field carp” (PF-carp), in a “globally important agricultural heritage system” (GIAHS), i.e., the 1,200-y-old rice–fish coculture system in Zhejiang Province, China. Our molecular and morphological analysis showed that the PF-carp has changed into a distinct local population with higher genetic diversity and diverse color types. Within this GIAHS region, PF-carps exist as a continuous metapopulation, although three genetic groups could be identified by microsatellite markers. Thousands of small farmer households interdependently obtained fry and parental carps for their own rice–fish production, resulting in a high gene flow and large numbers of parent carps distributing in a mosaic pattern in the region. Landscape genetic analysis indicated that farmers’ connectivity was one of the major factors that shaped this genetic pattern. Population viability analysis further revealed that the numbers of these interconnected small farmer households and their connection intensity affect the carps’ inherent genetic diversity. The practice of mixed culturing of carps with diverse color types helped to preserve a wide range of genetic resources in the paddy field. This widespread traditional practice increases fish yield and resource use, which, in return, encourages famers to continue their practice of selecting and conserving diverse color types of PF-carp. Our results suggested that traditional farmers secure the genetic diversity of PF-carp and its viability over generations in this region through interdependently incubating and mixed-culturing practices within the rice−fish system.

Conservation and genetic characterisation of common bean landraces from Cilento region (southern Italy): high differentiation in spite of low genetic diversity

Since its introduction from Central-South America to Italy almost 500 years ago, the common bean (Phaseolus vulgaris L.) was largely cultivated across the peninsula in hundreds of different landraces. However, globalisation and technological modernisation of agricultural practices in the last decades promoted the cultivation of few varieties at the expense of traditional and local agro-ecotypes, which have been confined to local markets or have completely disappeared. The aim of this study was to evaluate the genetic diversity and differentiation in 12 common bean landraces once largely cultivated in the Cilento region (Campania region, southern Italy), and now the object of a recovery program to save them from extinction. The analysis conducted using 13 nuclear microsatellite loci in 140 individuals revealed a high degree of homozygosity within each landrace and a strong genetic differentiation that was reflected in the success in assigning individuals to the source landrace. On the contrary, internal transcribed spacers 1 and 2, analysed in one individual per landrace, were highly similar among common bean landraces but allowed the identification of a cowpea variety (Vigna unguiculata Walp.), a crop largely cultivated in the Old World before the arrival of common bean from Americas. In conclusion, our study highlighted that conservation of landraces is important not only for the cultural and socio-economic value that they have for local communities, but also because the time and conditions in which they have been selected have led to that genetic distinctiveness that is at the basis of many potential agronomical applications and dietary benefits.

Genetic structure and isolation by altitude in rice landraces of Yunnan, China revealed by nucleotide and microsatellite marker polymorphisms

Rice landraces, a genetic reservoir for varietal improvement, are developed by farmers through artificial selection during the long-term domestication process. To efficiently conserve, manage, and use such germplasm resources, an understanding of the genetic structure and differentiation of local rice landraces is required. In this study, we analyzed 188 accessions of rice landraces collected from localities across an altitudinal gradient from 425 to 2, 274 m above sea level in Yunnan Province, China using ten target genes and 48 SSR markers. We detected clear differentiation of the rice landraces into indica and japonica groups and further separation of the accessions in each group into two subgroups according to altitude, including a lower altitude subgroup and higher altitude subgroup. The AMOVA results showed significant genetic differentiation among altitude zones at SSRs and most genes, except Os1977 and STS22. We further determined that differentiation among landrace populations followed a model of isolation by altitude, in which gene flow was higher among populations at similar altitude levels than across different altitude levels. Our findings demonstrated that both adaptation to altitude and altitude-dependent gene flow played key roles in the genetic differentiation of rice landraces in Yunnan, China.

Unexpected pattern of pearl millet genetic diversity among ethno-linguistic groups in the Lake Chad Basin

Despite of a growing interest in considering the role of sociological factors in seed exchanges and their consequences on the evolutionary dynamics of agro-biodiversity, very few studies assessed the link between ethno-linguistic diversity and genetic diversity patterns in small-holder farming systems. This is key for optimal improvement and conservation of crop genetic resources. Here, we investigated genetic diversity at 17 SSR markers of pearl millet landraces (varieties named by farmers) in the Lake Chad Basin. 69 pearl millet populations, representing 27 landraces collected in eight ethno-linguistic farmer groups, were analyzed. We found that the farmers' local taxonomy was not a good proxy for population's genetic differentiation as previously shown at smaller scales. Our results show the existence of a genetic structure of pearl millet mainly associated with ethno-linguistic diversity in the western side of the lake Chad. It suggests there is a limit to gene flow between landraces grown by different ethno-linguistic groups. This result was rather unexpected, because of the highly outcrossing mating system of pearl millet, the high density of pearl millet fields all along the green belt of this Sahelian area and the fact that seed exchanges among ethno-linguistic groups are known to occur. In the eastern side of the Lake, the pattern of genetic diversity suggests a larger efficient circulation of pearl millet genes between ethno-linguistic groups that are less numerous, spatially intermixed and, for some of them, more prone to exogamy. Finally, other historical and environmental factors which may contribute to the observed diversity patterns are discussed.

A high-throughput, modified ALS activity assay for Cyperus difformis and Schoenoplectus mucronatus seedlings

Cyperus difformis L. (CYPDI) and Schoenoplectus mucronatus (L.) Palla (SCHMU) are major weeds of California (CA) rice, where resistance to acetolactate synthase (ALS)-inhibitors was identified in several CYPDI and SCHMU populations that have also evolved resistance to photosystem II (PSII)-inhibiting herbicides. The mechanism of ALS resistance in these populations remains to be clarified but this information is crucial in a weed management program, especially in a scenario where resistance to multiple herbicides has been identified. ALS activity assays are commonly used to diagnose resistance to ALS-inhibitors, but protocols currently available are burdensome for the study of CYPDI and SCHMU, as they require large amounts of plant material from young seedlings and have low yields. Our objective was to investigate the ALS resistance mechanism in suspected ALS-resistant (R) CYPDI and SCHMU biotypes using a modified ALS activity assay that requires less plant material. ALS enzymes from suspected R biotypes were at least 10,000-fold less sensitive to bensulfuron-methyl than susceptible (S) cohorts, indicating ALS resistance that is likely due to an altered target-site. Protein concentration (mgg^-1 tissue) did not differ between R and S biotypes within each species, suggesting that R biotypes do not over produce ALS enzymes. CYPDI biotypes had up to 4-fold more protein per mg of tissue than SCHMU biotypes, but up to 7-fold more acetoin per mg^-1 protein was quantified in SCHMU, suggesting greater ALS catalytic ability in SCHMU biotypes, regardless of their herbicide resistance status. Our optimized protocol to measure ALS activity allowed for up to a 3-fold increase in the number of assays performed per g of leaf tissue. The modified assay may be useful for measuring ALS activity in other weed species that also produce small amount of foliage in early growth stages when protein in tissue is most abundant.

Genetic Diversity within a Global Panel of Durum Wheat (Triticum durum) Landraces and Modern Germplasm Reveals the History of Alleles Exchange

Durum wheat is the 10th most important crop in the world, and its use traces back to the origin of agriculture. Unfortunately, in the last century only part of the genetic diversity available for this species has been captured in modern varieties through breeding. Here, the population structure and genetic diversity shared among elites and landraces collected from 32 countries was investigated. A total of 370 entries were genotyped with Axiom 35K array to identify 8,173 segregating single nucleotide polymorphisms (SNPs). Of these, 500 were selected as highly informative with a PIC value above 0.32 and used to test population structure via DAPC, STRUCTURE, and neighbor joining tree. A total of 10 sub-populations could be identified, six constituted by modern germplasm and four by landraces of different geographical origin. Interestingly, genomic comparison among groups indicated that Middle East and Ethiopia had the lowest level of allelic diversity, while breeding programs and landraces collected outside these regions were the richest in rare alleles. Further, phylogenetic analysis among landraces indicated that Ethiopia might represent a second center of origin of durum wheat, rather than a second domestication site as previously believed. Together, the analyses carried here provide a global picture of the available genetic diversity for this crop and shall guide its targeted use by breeders.

Nuclear and Chloroplast DNA Variation Provides Insights into Population Structure and Multiple Origin of Native Aromatic Rices of Odisha, India

A large number of short grain aromatic rice suited to the agro-climatic conditions and local preferences are grown in niche areas of different parts of India and their diversity is evolved over centuries as a result of selection by traditional farmers. Systematic characterization of these specialty rices has not been attempted. An effort was made to characterize 126 aromatic short grain rice landraces, collected from 19 different districts in the State of Odisha, from eastern India. High level of variation for grain quality and agronomic traits among these aromatic rices was observed and genotypes having desirable phenotypic traits like erect flag leaf, thick culm, compact and dense panicles, short plant stature, early duration, superior yield and grain quality traits were identified. A total of 24 SSR markers corresponding to the hyper variable regions of rice chromosomes were used to understand the genetic diversity and to establish the genetic relationship among the aromatic short grain rice landraces at nuclear genome level. SSR analysis of 126 genotypes from Odisha and 10 genotypes from other states revealed 110 alleles with an average of 4.583 and the Nei’s genetic diversity value (He) was in the range of 0.034–0.880 revealing two sub-populations SP 1 (membership percentage-27.1%) and SP 2 (72.9%). At the organelle genomic level for the C/A repeats in PS1D sequence of chloroplasts, eight different plastid sub types and 33 haplotypes were detected. The japonica (Nipponbare) subtype (6C7A) was detected in 100 genotypes followed by O. rufipogon (KF428978) subtype (6C6A) in 13 genotypes while indica (93–11) sub type (8C8A) was seen in 14 genotypes. The tree constructed based on haplotypes suggests that short grain aromatic landraces might have independent origin of these plastid subtypes. Notably a wide range of diversity was observed among these landraces cultivated in different parts confined to the State of Odisha.

A psbA mutation (Val219 to Ile) causes resistance to propanil and increased susceptibility to bentazon in Cyperus difformis

BACKGROUND

Propanil-resistant (R) Cyperus difformis populations were recently confirmed in California rice fields. To date, propanil resistance in other weed species has been associated with enhanced aryl acylamidase (AAA)-mediated propanil conversion into 3,4-dichloroaniline. Our objectives were to determine the level of propanil resistance and cross-resistance to other PSII inhibitors in C. difformis lines, and to elucidate the mechanism of propanil resistance.

RESULTS

The propanil-R line had a 14-fold propanil resistance and increased resistance to bromoxynil, diuron and metribuzin, but not to atrazine. The R line, however, displayed a fourfold increased susceptibility to bentazon. Interestingly, susceptible (S) plants accumulated more 3,4-dichloroaniline and were more injured by propanil and carbaryl (AAA-inhibitor) applications than R plants, suggesting that propanil metabolism is not the resistance mechanism. psbA gene sequence analysis indicated a valine-219-isoleucine (Val219 Ile) amino acid exchange in the propanil-R chloroplast D1 protein.

CONCLUSION

The D1 Val219 Ile modification in C. difformis causes resistance to propanil, diuron, metribuzin and bromoxynil but increased susceptibility to bentazon, suggesting that the Val219 residue participates in binding of these herbicides. This is the first report of a higher plant exhibiting target-site propanil resistance. Tank mixing of bentazon and propanil, where permitted, can control both propanil-R and propanil-S C. difformis and prevent the spread of the resistant phenotype. © 2016 Society of Chemical Industry.

Differentiation and description of aromatic short grain rice landraces of eastern Indian state of Odisha based on qualitative phenotypic descriptors

Background

Speciality rice, in general, and aromatic rice in particular, possess enormous market potential for enhancing farm profits. However, systematic characterization of the diversity present in this natural wealth is a major pre requisite for using it in the breeding programs. This study reports qualitative phenotypic trait based characterization of 126 short grain aromatic rice genotypes, collected from different areas of the state of Odisha, India.

Results

Out of the 24 descriptors employed, highest variability (8 different types) was observed for lemma-palea colour with a genetic diversity index (He) of 0.696. The principal component analysis reveals that the tip colour of lemma, colour of awn and colour of stigma, cumulatively explain 74 % of the total variation. The Population STRUCTURE analysis classified the population into two subpopulations which were subdivided further into four distinct groups. The western and southern districts of Odisha are endowed with maximum diversity in comparison to eastern and northern districts and at district level comparisons, Koraput and Puri districts are rich with a genetic diversity values of 0.324 and 0.303 respectively. With this set of morphological qualitative traits, based on ‘phenoprinting’, a newly proposed bar coding system, unique fingerprints of each genotype can be effectively generated that can help in easy identification of these genotypes.

Conclusion

Though aromatic rices represent a tiny fraction of the total rice germplasm, a small collection of 126 land races did exhibit rich diversity for all the qualitative traits. For lemma-palea colour, eight different types were detected while for tip colour of lemma, six different types were recorded, suggesting the presence of rich variability in short grain aromatic rices that are conserved in this region. The proposed ‘phenoprinting’ can be an effective descriptor with the unique finger prints generated for each genotype and coupled with molecular (DNA) finger printing, we can discriminate and identify each and every aromatic short grain rice genotype. The proposed system not only help in conservation but also can confer IPR protection to these specialty rices.

Electronic supplementary material

The online version of this article (doi:10.1186/s12898-016-0086-8) contains supplementary material, which is available to authorized users.

Genetic diversity and population structure of 'Khao Kai Noi', a Lao rice (Oryza sativa L.) landrace, revealed by microsatellite DNA markers

Rice (Oryza sativa L.) is the main food for people in Laos, where it has been grown and eaten since prehistory. Diverse landraces are grown in Laos. 'Khao Kai Noi', a landrace favored for its eating quality, is held in the nationwide collection of traditional landraces in the Lao national genebank. Genetic diversity is crucial for sustainable use of genetic resources and conservation. To investigate the genetic diversity of 'Khao Kai Noi' for conservation, we genotyped 70 accessions by using 23 polymorphic simple sequence repeat markers. The markers generated 2 to 17 alleles (132 in total), with an average of 5.7 per locus. The total expected heterozygosity over all 'Khao Kai Noi' accessions was 0.271. Genetic variation was largest among accessions and smallest within accessions. Khao Kai Noi accessions were classified into three different genetic backgrounds, but there was unclear association between the three inferred population and name subgroups and geographical distribution. Most of the accessions were clustered with temperate japonica and showed genetic relatedness to rice from neighboring provinces of Vietnam, suggesting a Vietnamese origin. The results of this study will contribute to the conservation, core collection and future breeding of the Khao Kai Noi population.

Geographical distribution of genetic diversity in Secale landrace and wild accessions

BACKGROUND

Rye, Secale cereale L., has historically been a crop of major importance and is still a key cereal in many parts of Europe. Single populations of cultivated rye have been shown to capture a large proportion of the genetic diversity present in the species, but the distribution of genetic diversity in subspecies and across geographical areas is largely unknown. Here we explore the structure of genetic diversity in landrace rye and relate it to that of wild and feral relatives.

RESULTS

A total of 567 SNPs were analysed in 434 individuals from 76 accessions of wild, feral and cultivated rye. Genetic diversity was highest in cultivated rye, slightly lower in feral rye taxa and significantly lower in the wild S. strictum Presl. and S. africanum Stapf. Evaluation of effects from ascertainment bias suggests underestimation of diversity primarily in S. strictum and S. africanum. Levels of ascertainment bias, STRUCTURE and principal component analyses all supported the proposed classification of S. africanum and S. strictum as a separate species from S. cereale. S. afghanicum (Vav.) Roshev, S. ancestrale Zhuk., S. dighoricum (Vav.) Roshev, S. segetale (Zhuk.) Roshev and S. vavilovii Grossh. seemed, in contrast, to share the same gene pool as S. cereale and their genetic clustering was more dependent on geographical origin than taxonomic classification. S. vavilovii was found to be the most likely wild ancestor of cultivated rye. Among cultivated rye landraces from Europe, Asia and North Africa five geographically discrete genetic clusters were identified. These had only limited overlap with major agro-climatic zones. Slash-and-burn rye from the Finnmark area in Scandinavia formed a distinct cluster with little similarity to other landrace ryes. Regional studies of Northern and South-West Europe demonstrate different genetic distribution patterns as a result of varying cultivation intensity.

CONCLUSIONS

With the exception of S. strictum and S. africanum different rye taxa share the majority of the genetic variation. Due to the vast sharing of genetic diversity within the S. cereale clade, ascertainment bias seems to be a lesser problem in rye than in predominantly selfing species. By exploiting within accession diversity geographic structure can be shown on a much finer scale than previously reported.

Diachronic analysis of genetic diversity in rice landraces under on-farm conservation in Yunnan, China

Diachronic analysis showed no significant changes in the level of genetic diversity occurred over the past 27 years' domestication, which indicated genetic diversity was successfully maintained under on-farm conservation. Rice (Oryza sativa L.) is one of the earliest domesticated crop species. Its genetic diversity has been declining as a result of natural and artificial selection. In this study, we performed the first analysis of the levels and patterns of nucleotide variation in rice genomes under on-farm conservation in Yunnan during a 27-year period of domestication. We performed large-scale sequencing of 600 rice accessions with high diversity, which were collected in 1980 and 2007, using ten unlinked nuclear loci. Diachronic analysis showed no significant changes in the level of genetic diversity occurring over the past 27 years' domestication, which indicated genetic diversity was successfully maintained under on-farm conservation. Population structure revealed that the rice landraces could be grouped into two subpopulations, namely the indica and japonica groups. Interestingly, the alternate distribution of indica and japonica rice landraces could be found in each ecological zone. The results of AMOVA showed that on-farm conservation provides opportunities for continued differentiation and variation of landraces. Therefore, dynamic conservation measures such as on-farm conservation (which is a backup, complementary strategy to ex situ conservation) should be encouraged and enhanced, especially in crop genetic diversity centers. The results of this study offered accurate insights into short-term evolutionary processes and provided a scientific basis for on-farm management practices.

Genetic Diversity and Population Structure of Collard Landraces and their Relationship to Other Brassica oleracea Crops

Landraces have the potential to provide a reservoir of genetic diversity for crop improvement to combat the genetic erosion of the food supply. A landrace collection of the vitamin-rich specialty crop collard (Brassica oleracea L. var. viridis) was genetically characterized to assess its potential for improving the diverse crop varieties of B. oleracea. We used the Illumina 60K Brassica SNP BeadChip array with 52,157 single nucleotide polymorphisms (SNPs) to (i) clarify the relationship of collard to the most economically important B. oleracea crop types, (ii) evaluate genetic diversity and population structure of 75 collard landraces, and (iii) assess the potential of the collection for genome-wide association studies (GWAS) through characterization of genomic patterns of linkage disequilibrium. Confirming the collection as a valuable genetic resource, the collard landraces had twice the polymorphic markers (11,322 SNPs) and 10 times the variety-specific alleles (521 alleles) of the remaining crop types examined in this study. On average, linkage disequilibrium decayed to background levels within 600 kilobase (kb), allowing for sufficient coverage of the genome for GWAS using the physical positions of the 8273 SNPs polymorphic among the landraces. Although other relationships varied, the previous placement of collard with the cabbage family was confirmed through phylogenetic analysis and principal coordinates analysis (PCoA).

Genetic diversity and population structure of an Italian landrace of runner bean (Phaseolus coccineus L.): inferences for its safeguard and on-farm conservation

The landraces are considered important sources of valuable germplasm for breeding activities to face climatic changes as well as to satisfy the requirement of new varieties for marginal areas. Runner bean (Phaseolus coccineus L.) is one of the most cultivated Phaseolus species worldwide, but few studies have been addressed to assess the genetic diversity and structure within and among landrace populations. In the present study, 20 different populations of a runner bean landrace from Central Italy named "Fagiolone," together with 41 accessions from Italy and Mesoamerica, were evaluated by using 14 nuclear SSRs to establish its genetic structure and distinctiveness. Results indicated that "Fagiolone" landrace can be considered as a dynamic evolving open-pollinated population that shows a significant level of genetic variation, mostly detected within populations, and the presence of two main genetic groups, of which one distinguished from other Italian runner bean landraces. Results highlighted also a relevant importance of farmers' management practices able to influence the genetic structure of this landrace, in particular the seed exchanges and selection, and the past introduction in cultivation of landraces/cultivars similar to seed morphology, but genetically rather far from "Fagiolone." The most suitable on-farm strategies for seed collection, conservation and multiplication will be defined based on our results, as a model for threatened populations of other allogamous crop species. STRUCTURE and phylogenetic analyses indicated that Mesoamerican accessions and Italian landraces belong to two distinct gene pools confirming the hypothesis that Europe could be considered a secondary diversification center for P. coccineus.

European flint landraces grown in situ reveal adaptive introgression from modern maize

We have investigated the role of selection in the determination of the detected levels of introgression from modern maize hybrid varieties into maize landraces still cultivated in situ in Italy. We exploited the availability of a historical collection of landraces undertaken before the introduction and widespread use of modern maize, to analyse genomic changes that have occurred in these maize landraces over 50 years of co-existence with hybrid varieties. We have combined a previously published SSR dataset (n=21) with an AFLP loci dataset (n=168) to provide higher resolution power and to obtain a more detailed picture. We show that selection pressures for adaptation have favoured new alleles introduced by migration from hybrids. This shows the potential for analysis of historical introgression even over this short period of 50 years, for an understanding of the evolution of the genome and for the identification of its functionally important regions. Moreover, this demonstrates that landraces grown in situ represent almost unique populations for use for such studies when the focus is on the domesticated plant. This is due to their adaptation, which has arisen from their dynamic evolution under a continuously changing agro-ecological environment, and their capture of new alleles from hybridisation. We have also identified loci for which selection has inhibited introgression from modern germplasm and has enhanced the distinction between landraces and modern maize. These loci indicate that selection acted in the past, during the formation of the flint and dent gene pools. In particular, the locus showing the strongest signals of selection is a Misfit transposable element. Finally, molecular characterisation of the same samples with two different molecular markers has allowed us to compare their performances. Although the genetic-diversity and population-structure analyses provide the same global qualitative pattern, which thus provides the same inferences, there are differences related to their natures and characteristics.

Inference of domestication history and differentiation between early- and late-flowering varieties in pearl millet

Pearl millet (Pennisetum glaucum) is a staple crop in Sahelian Africa. Farmers usually grow varieties with different cycle lengths and complementary functions in Sahelian agrosystems. Both the level of genetic differentiation of these varieties and the domestication history of pearl millet have been poorly studied. We investigated the neutral genetic diversity and population genetic structure of early- and late-flowering domesticated and wild pearl millet populations using 18 microsatellite loci and 8 nucleotide sequences. Strikingly, early- and late-flowering domesticated varieties were not differentiated over their whole distribution area, despite a clear difference in their isolation-by-distance pattern. Conversely, our data brought evidence for two well-differentiated genetic pools in wild pearl millet, allowing us to test scenarios with different numbers and origins of domestication using approximate Bayesian computation (ABC). The ABC analysis showed the likely existence of asymmetric migration between wild and domesticated populations. The model choice procedure indicated that a single domestication from the eastern wild populations was the more likely scenario to explain the polymorphism patterns observed in cultivated pearl millet.

Towards a comprehensive characterization of durum wheat landraces in Moroccan traditional agrosystems: analysing genetic diversity in the light of geography, farmers' taxonomy and tetraploid wheat domestication history

BACKGROUND

Crop diversity managed by smallholder farmers in traditional agrosystems is the outcome of historical and current processes interacting at various spatial scales, and influenced by factors such as farming practices and environmental pressures. Only recently have studies started to consider the complexity of these processes instead of simply describing diversity for breeding purposes. A first step in that aim is to add multiple references to the collection of genetic data, including the farmers' varietal taxonomy and practices and the historical background of the crop.

RESULTS

On the basis of interview data collected in a previous study, we sampled 166 populations of durum wheat varieties in two traditional Moroccan agrosystems, in the Pre-Rif and Atlas Mountains regions. Using a common garden experiment, we detected a high phenotypic variability on traits indicative of taxonomical position and breeding status, namely spike shape and plant height. Populations often combined modern (short) with traditional-like (tall) statures, and classical durum squared spike shape (5 flowers/spikelet) with flat spike shape (3 flowers/ spikelet) representative of primitive domesticated tetraploid wheat (ssp. dicoccum). By contrast, the genetic diversity assessed using 14 microsatellite markers was relatively limited. When compared to the genetic diversity found in a large collection of tetraploid wheat, it corresponded to free-threshing tetraploid wheat. Within Morocco, the two studied regions differed for both genetic diversity and variety names. Within regions, neither geography nor variety names nor even breeding status constituted strong barriers to gene exchange despite a few significant patterns.

CONCLUSIONS

This first assessment of morphological and genetic diversity allowed pointing out some important factors that may have influenced the structure and evolutionary dynamics of durum wheat in Morocco: the significance of variety names, the occurrence of mixtures within populations, the relative strength of seed exchange between farmers and local adaptation, as well as the fate of modern varieties once they have been introduced. Further, multidisciplinary studies at different spatial scales are needed to better understand these complex agrosystems of invaluable importance for food security.

Seed-mediated gene flow promotes genetic diversity of weedy rice within populations: implications for weed management

Increased infestation of weedy rice-a noxious agricultural pest has caused significant reduction of grain yield of cultivated rice (Oryza sativa) worldwide. Knowledge on genetic diversity and structure of weedy rice populations will facilitate the design of effective methods to control this weed by tracing its origins and dispersal patterns in a given region. To generate such knowledge, we studied genetic diversity and structure of 21 weedy rice populations from Sri Lanka based on 23 selected microsatellite (SSR) loci. Results indicated an exceptionally high level of within-population genetic diversity (He = 0.62) and limited among-population differentiation (Fst = 0.17) for this predominantly self-pollinating weed. UPGMA analysis showed a loose genetic affinity of the weedy rice populations in relation to their geographical locations, and no obvious genetic structure among populations across the country. This phenomenon was associated with the considerable amount of gene flow between populations. Limited admixture from STRUCTURE analyses suggested a very low level of hybridization (pollen-mediated gene flow) between populations. The abundant within-population genetic diversity coupled with limited population genetic structure and differentiation is likely caused by the considerable seed-mediated gene flow of weedy rice along with the long-distance exchange of farmer-saved rice seeds between weedy-rice contaminated regions in Sri Lanka. In addition to other effective weed management strategies, promoting the application of certified rice seeds with no weedy rice contamination should be the immediate action to significantly reduce the proliferation and infestation of this weed in rice ecosystems in countries with similar rice farming styles as in Sri Lanka.

Anchoring durum wheat diversity in the reality of traditional agricultural systems: varieties, seed management, and farmers' perception in two Moroccan regions

BACKGROUND

Traditional agrosystems are the places were crop species have evolved and continue to evolve under a combination of human and environmental pressures. A better knowledge of the mechanisms underlying the dynamics of crop diversity in these agrosystems is crucial to sustain food security and farmers' self-reliance. It requires as a first step, anchoring a description of the available diversity in its geographical, environmental, cultural and socio-economic context.

METHODS

We conducted interviews with farmers cultivating durum wheat in two contrasted traditional agrosystems of Morocco in the Pre-Rif (163 farmers) and in the oases of the Atlas Mountains (110 farmers). We documented the varietal diversity of durum wheat, the main characteristics of the farms, the farming and seed management practices applied to durum wheat, and the farmers' perception of their varieties.

RESULTS

As expected in traditional agrosystems, farmers largely practiced diversified subsistence agriculture on small plots and relied on on-farm seed production or informal seed exchange networks. Heterogeneity nevertheless prevailed on many variables, especially on the modernization of practices in the Pre-Rif region. Fourteen (resp. 11) traditional and 5 (resp. 3) modern varieties were identified in the Pre-Rif region (resp. in the Atlas Mountains). The majority of farmers grew a single variety, and most traditional varieties were distributed in restricted geographical areas. At the farm level, more than half of the varieties were renewed in the last decade in the Pre-Rif, a more rapid renewal than in the Atlas Mountain. Modern varieties were more prevalent in the Pre-Rif region and were integrated in the traditional practices of seed production, selection and exchange. They were clearly distinguished by the farmers from the landraces, the last ones being appreciated for their quality traits.

CONCLUSIONS

The surveyed traditional agrosystems constitute open, dynamic and heterogeneous entities. We suggest that competing factors could favour or limit the cultivation of improved varieties and the erosion of original durum wheat diversity. This first description opens the way to focused further investigations, including complementing variety names with cultural, genetic and phenotypic information and unravelling the multidimensional factors and consequences of modern variety adoption.

Processes underpinning development and maintenance of diversity in rice in West Africa: evidence from combining morphological and molecular markers

We assessed the interplay of artificial and natural selection in rice adaptation in low-input farming systems in West Africa. Using 20 morphological traits and 176 molecular markers, 182 farmer varieties of rice (Oryza spp.) from 6 West African countries were characterized. Principal component analysis showed that the four botanical groups (Oryza sativa ssp. indica, O. sativa ssp. japonica, O. glaberrima, and interspecific farmer hybrids) exhibited different patterns of morphological diversity. Regarding O. glaberrima, morphological and molecular data were in greater conformity than for the other botanical groups. A clear difference in morphological features was observed between O. glaberrima rices from the Togo hills and those from the Upper Guinea Coast, and among O. glaberrima rices from the Upper Guinea Coast. For the other three groups such clear patterns were not observed. We argue that this is because genetic diversity is shaped by different environmental and socio-cultural selection pressures. For O. glaberrima, recent socio-cultural selection pressures seemed to restrict genetic diversity while this was not observed for the other botanical groups. We also show that O. glaberrima still plays an important role in the selection practices of farmers and resulting variety development pathways. This is particularly apparent in the case of interspecific farmer hybrids where a relationship was found between pericarp colour, panicle attitude and genetic diversity. Farmer varieties are the product of long and complex trajectories of selection governed by local human agency. In effect, rice varieties have emerged that are adapted to West African farming conditions through genotype × environment × society interactions. The diversity farmers maintain in their rice varieties is understood to be part of a risk-spreading strategy that also facilitates successful and often serendipitous variety innovations. We advocate, therefore, that farmers and farmer varieties should be more effectively involved in crop development.

Population structure of barley landrace populations and gene-flow with modern varieties

Landraces are heterogeneous plant varieties that are reproduced by farmers as populations that are subject to both artificial and natural selection. Landraces are distinguished by farmers due to their specific traits, and different farmers often grow different populations of the same landrace. We used simple sequence repeats (SSRs) to analyse 12 barley landrace populations from Sardinia from two collections spanning 10 years. We analysed the population structure, and compared the population diversity of the landraces that were collected at field level (population). We used a representative pool of barley varieties for diversity comparisons and to analyse the effects of gene flow from modern varieties. We found that the Sardinian landraces are a distinct gene pool from those of both two-row and six-row barley varieties. There is also a low, but significant, mean level and population-dependent level of introgression from the modern varieties into the Sardinian landraces. Moreover, we show that the Sardinian landraces have the same level of gene diversity as the representative sample of modern commercial varieties grown in Italy in the last decades, even within population level. Thus, these populations represent crucial sources of germplasm that will be useful for crop improvement and for population genomics studies and association mapping, to identify genes, loci and genome regions responsible for adaptive variations. Our data also suggest that landraces are a source of valuable germplasm for sustainable agriculture in the context of future climate change, and that in-situ conservation strategies based on farmer use can preserve the genetic identity of landraces while allowing adaptation to local environments.

Current issues in cereal crop biodiversity

The exploration, conservation, and use of agricultural biodiversity are essential components of efficient transdisciplinary research for a sustainable agriculture and food sector. Most recent advances on plant biotechnology and crop genomics must be complemented with a holistic management of plant genetic resources. Plant breeding programs aimed at improving agricultural productivity and food security can benefit from the systematic exploitation and conservation of genetic diversity to meet the demands of a growing population facing climate change. The genetic diversity of staple small grains, including rice, maize, wheat, millets, and more recently quinoa, have been surveyed to encourage utilization and prioritization of areas for germplasm conservation. Geographic information system technologies and spatial analysis are now being used as powerful tools to elucidate genetic and ecological patterns in the distribution of cultivated and wild species to establish coherent programs for the management of plant genetic resources for food and agriculture.

Comparative study of endophytic and endophytic diazotrophic bacterial communities across rice landraces grown in the highlands of northern Thailand

Communities of bacterial endophytes within the rice landraces cultivated in the highlands of northern Thailand were studied using fingerprinting data of 16S rRNA and nifH genes profiling by polymerase chain reaction-denaturing gradient gel electrophoresis. The bacterial communities' richness, diversity index, evenness, and stability were varied depending on the plant tissues, stages of growth, and rice cultivars. These indices for the endophytic diazotrophic bacteria within the landrace rice Bue Wah Bo were significantly the lowest. The endophytic bacteria revealed greater diversity by cluster analysis with seven clusters compared to the endophytic diazotrophic bacteria (three clusters). Principal component analysis suggested that the endophytic bacteria showed that the community structures across the rice landraces had a higher stability than those of the endophytic diazotrophic bacteria. Uncultured bacteria were found dominantly in both bacterial communities, while higher generic varieties were observed in the endophytic diazotrophic bacterial community. These differences in bacterial communities might be influenced either by genetic variation in the rice landraces or the rice cultivation system, where the nitrogen input affects the endophytic diazotrophic bacterial community.