Eco-geographical Adaptation Research Articles

LHD3 Encoding a J-Domain Protein Controls Heading Date in Rice

Heading date is one of the most important agronomic traits of rice, which critically affects rice ecogeographical adaptation, yield and quality. In this study, a late heading date 3 (lhd3) mutant was screened from the 60Co-γ irradiation mutant library. The lhd3 delayed heading date in rice under both short day and long day conditions. Map-based cloning combined with Mutmap strategy was adopted to isolate the causal LHD3 gene. The LHD3 gene encodes a DNA_J domain protein, which was ubiquitously expressed in various plant organs, and dominant expressed in stems and leaves. Subcellular localization analysis showed that LHD3 was localized to nucleus, indicating that LHD3 may interact with other elements to regulate the expression of flowering genes. The transcriptions of the heading activators Ehd1, Hd3a and RFT1 significantly decreased in the lhd3 mutant, suggesting that LHD3 may control the heading date through the Ehd1-Hd3a/RFT1 photoperiodic flowering pathway. The variation and haplotype analyses of the genomic region of LHD3 showed that there were 7 haplotypes in the LHD3 region from 4 702 accessions. The haplotypes of LHD3 can be divided into two classes: class a and class b, and the heading dates of these two classes were significantly different. Further study showed that two single nucleotide polymorphisms (SNPs), SNP10 (G2100C) in Hap II and SNP3 (C861T) in Hap VII, may be the functional sites causing early and late heading in accessions. Nucleotide diversity analysis showed LHD3 had been selected in the indica population, rather than in the japonica population. Therefore, the present study sheds light on the regulation of LHD3 on heading date in rice and suggests that LHD3 is a novel promising new target for rice molecular design and breeding improvement.

Ecogeographical Adaptation Revisited: Morphological Variations in the Plateau Brown Frog along an Elevation Gradient on the Qinghai-Tibetan Plateau.

Simple SummaryA number of studies have explored how the body size and extremities of frogs vary in response to the changing environmental conditions across different geographical gradients, but the outcomes remain controversial. Here, we studied the morphological variations of the plateau brown frog (Rana kukunoris) along an elevation gradient (~1800–3500 m) on the eastern margin of the Qinghai–Tibetan Plateau to understand how environmental and biological factors affect them, and to assess whether these variations help to improve thermoregulation. Although we found that male and female frogs showed different variations in body size and extremities along the elevational gradient, both of them showed a significant decrease in the ratio of extremities to body size with increasing elevation. The decreasing ratio implies a gain of thermoregulatory benefits based on the ecogeographical rules. Moreover, the morphological variations were found to be strongly related to both environmental and biological factors. These results suggest that ecogeographical adaptation in frogs may be more complicated than other terrestrial vertebrate species. Most importantly, the adaptation should be viewed as a result of both environmental and biological factors, while it may also appear as an interactive change between body size and extremities.Several anurans have broad elevational and latitudinal distribution ranges; distinct species and populations may face various environmental and selection stresses. Due to their environmental sensitivity, adaptation is critical for the long-term persistence of anurans. Previous studies have tried to identify the ecogeographical pattern and its mechanism in anurans, suggesting different patterns, but the related explanatory mechanisms are yet to be generally supported and are suggested to be complicated. To explore the elusive mechanisms, we studied the morphological variation of the plateau brown frog (Rana kukunoris) along an elevational gradient on the eastern margin of the Qinghai–Tibetan Plateau. Using body size, extremity length, and the ratio between them (extremities/body size) as testing indicators, we examined potential ecogeographical adaptations and investigated how environmental and biological factors could shape the morphological development in R. kukunoris. We found that males and females showed different variations in body size and extremities along the elevational gradient, whereas both of them showed a decreasing extremities/body size ratio along elevation. Together with the strong correlations between environmental and biological factors and the morphometrics, we identified ecogeographical adaptation and a sexual difference in the selective pressures on the extremities and body size of the plateau brown frog. Our results imply that geographic variations in anuran morphological traits should be understood as an outcome of environmental and biological factors. Furthermore, ecogeographical adaptation in anurans can manifest as an interactive change between body size and extremities.

Detection of quantitative trait loci for heading date and temperature responsiveness in a re‐sequenced, recombinant inbred line of japonica rice from Heilongjiang province, china

AbstractThe hereditary basis and identification of novel genes of heading date have significant implications for japonica rice improvement in northeast China, especially in Heilongjiang province. A re‐sequenced recombinant inbred line (RIL) population derived from the cross between Lijiangxintuanheigu (LTH) and Shennong 265 (SN265) was used to detect the genetic basis for the RIL in 2017 and 2018. Fourteen heading date quantitative trait loci (QTLs), including nine in 2017 and thirteen in 2018, were detected with a linkage map containing 2,818 bin markers. They were distributed on chromosomes 3, 4, 6 and 9–11 with 9.34%–25.26% phenotypic variations. The QTLs qHD3a, qHD4a, qHD4b, qHD4c, qHD9b, qHD10, qHD11c and qHD11d were identified in both years. The qTRS1, qTRS3a (qHD3a), qTRS3b (qHD3b) and qTRS9 (qHD9a) alleles from LTH and the qTRS4 allele from SN265 were identified by controlling the temperature responsiveness in the RIL population. The explained phenotypic variation in these five QTLs varied from 14.52% to 26.31%. In order to accurately determine the difference in heading date under different temperature conditions, the RILs and two parents were grown in a phytotron. Four QTLs controlling temperature responsiveness were identified on chromosomes 3, 6 and 9, including qTRS3a (qHD3a), qTRS3b (qHD3b), qTRS6 and qTRS9 (qHD9a). In a different environment, qTRS3a (qHD3a), qTRS3b (qHD3b) and qTRS9 (qHD9a) were detected. A comparison of chromosomal locations between the QTLs detected in this study and heading date genes previously cloned indicated that DTH3, Hd16, RFL, HAF1, Ehd2 and RBS1 might be candidate genes for them. The four major heading date genes (Hd1, Ghd7, Ghd7.1 and Ghd8) affecting ecogeographical adaptation were sequenced between SN265 and LTH. SN265 carried a functional Hd1 haplotype, a weak functional Ghd7 haplotype, a weak functional Ghd7.1 haplotype and a weak functional Ghd8 haplotype. LTH also carried functional Hd1 haplotype, a weak functional Ghd7 haplotype, a non‐functional Ghd7.1 haplotype and a non‐functional Ghd8 haplotype. The combinations of the Hd1, Ghd7, Ghd7.1 and Ghd8 alleles in SN265 and LTH largely defined their short heading date under long‐day conditions. The selection of heading date gene combinations with functional Hd1 alleles and non‐functional alleles or weak functional alleles of Ghd7, Ghd7.1 and Ghd8 would be an effective way to improve japonica rice with proper heading days in Northeast China. The novel QTLs detected in this study could also become a valuable source for designing the appropriate heading date in Northeast China japonica rice.

Ghd8 controls rice photoperiod sensitivity by forming a complex that interacts with Ghd7

BackgroundFlowering time is one of the most important agronomic characteristics that ultimately determine yield potential and eco-geographical adaptation in crops. Ghd8 and Ghd7, two major flowering genes, have similar functions and large pleiotropic effects in controlling the heading date, plant height and grain yield of rice. However, these gene interactions at the genetic and molecular levels have not been determined to date.ResultsIn this study, we investigated the genetic interaction between Ghd8 and Ghd7 by using a set of near-isogenic lines and a panel of natural germplasm accessions in rice. We found that Ghd8 affected multiple agronomic traits in a functional Ghd7-dependent manner. Both functional Ghd8 and Ghd7 are pivotal for rice photoperiod sensitivity controlled by Hd1 and Hd3a. GHD8 could form a heterotrimeric complex with HD1 and OsHAP5b to activate the transcription of Ghd7 by binding directly to the promoter region of Ghd7, which contains the CCAAT-box motif.ConclusionsThe results of this study help to elucidate the genetic and molecular bases of Ghd8 and Ghd7 interactions, indicating that Ghd8 acts upstream of Ghd7 to activate its transcription, which inhibits Hd3a expression and thus affects flowering time and rice adaptation.

The genetic structure of flax illustrates environmental and anthropogenic selections that gave rise to its eco-geographical adaptation

Flax, one of the eight founder crops of agriculture, has been cultivated for its oil and/or fiber for millennia. Understanding genetic divergence and geographic origins of germplasm in line with their cultivation history and ecological adaptation are essential for conservation and breeding. Here we performed a genome-wide assessment based on more than 51,000 single nucleotide polymorphic sites defining 383 flax accessions from a core collection representing 37 flax growing countries. Population structure analysis resulted in a total of 12 populations that were pooled into four major groups: Temperate, South Asian, Abyssinian and Mediterranean. The vast majority (n = 335) belonged to the Temperate group that comprised eight populations including one dominated by fiber flax. Genetic variation between fiber and oil morphotypes was less pronounced than variation within morphotypes. The genetic variation among groups and populations was attributed in part to eco-geographic and anthropogenic factors. Genetic signatures indicated loci under strong selection by environmental factors such as day length. A high concentration of private haplotypes were observed in the South Asian, Mediterranean and Abyssinian populations despite their low genotype representation, hinting at the long history of the crop in these regions. The addition of genotypes from these three regions would enrich the core collection by capturing a wider genetic breadth for breeding and conservation.

Natural variation at qHd1 affects heading date acceleration at high temperatures with pleiotropism for yield traits in rice

BackgroundRice is highly sensitive to temperature fluctuations. Recently, the frequent occurrence of high temperature stress has heavily influenced rice production. Proper heading date in specific environmental conditions could ensure high grain yield. Rice heading greatly depends on the accurate measurement of environmental changes, particularly in day length and temperature. In contrary to the detailed understanding of the photoperiod pathway, little has been known about how temperature regulates the genetic control of rice heading.ResultsNear isogenic lines that were segregated for qHd1, were developed from a cross between indica rice varieties Zhenshan 97 (ZS97) and Milyang 46 (MY46). Using a five sowing-date experiment in the paddy field, we observed the involvement of qHd1 in temperature responses. With the gradual increase of temperature from Trial I to V, heading date of MY46 homozygotes continued to decrease for about 5 d per trial from 76 to 58 d, while that of ZS97 homozygotes was promoted at the same rate from Trial I to III and then stabilized at 69 d. This thermal response was confirmed in a temperature-gradient experiment conducted in the phytotron. It is also found that tolerance of the ZS97 allele to heading acceleration at high temperature was associated with higher grain weight that resulted in higher grain yield. Then, by qRT-PCR and RNA-seq, we found the pathway OsMADS51-Ehd1-RFT1/Hd3a underlying the qHd1-mediated floral response to temperature. By sequence comparison, OsMADS51 for qHd1 displayed a 9.5-kb insertion in the 1st intron of the ZS97 allele compared to the MY46 allele. Furthermore, this large insertion is commonly found in major early-season indica rice varieties, but not in the middle- and late-season ones, which corresponds to the requirement for high-temperature tolerance during the heading and grain-filling stages of early-season rice.ConclusionsBeneficial alleles at qHd1 confer tolerance to high temperatures at the heading and grain-filling stages, playing a significant role in the eco-geographical adaptation of early-season indica rice during modern breeding. These results, together with the underlying OsMADS51-Ehd1-RFT1/Hd3a floral pathway, provide valuable information for better understanding the molecular mechanism of temperature responsive regulation of heading date and yield traits in rice.

Progress in understanding molecular genetic basis of heterosis in rice

The exploitation of rice heterosis has made great success in China in the last 40 years. Since 1990s, a series of progress has been made in the dissection of genetic basis of rice heterosis. Different hybrid systems such as three-line hybrid and two-line hybrid have been included into heterosis study. Moreover, all kinds of hybrids including indica intra-subspecies hybrid, japonica intra-subspecies hybrid and inter-subspecies hybrid were widely used for generating populations. Based on various populations such as diallelcross design, F2:3, backcross population, “immortalized F2” population, and collection of commercial hybrids, evidences at the level of molecular genetics were obtained to support the hypotheses for genetic basis of heterosis such as dominance, overdominance and epistasis in rice, which all play important roles in controlling heterosis. The importance of each genetic component varied with hybrids either in intra-subspecific or inter-subspecific hybrids or even in different traits in the same hybrid. However, at single gene level, none of dozens of known functional genes exhibited overdominance in rice. The inconsistent results between population level and single gene level probably indicate that overdominance is dependent on genomic background. Pure genetic background likely eliminated overdominance by blocking gene interaction. In addition, no single-gene overdominance was in agreement with the fact that it is not easy to develophybrids with strong heterosis because it is expected that single-gene overdominance should make hybrids possessing better parent heterosis. Besides QTL for agronomy traits, other types of traits such as metabolites and gene expression were also used for QTL mapping, and amounts of resources were available. Data from multiple omics such as genomics (including DNA marker and quantitative trait loci), metabolomics and transcriptomics provided chance to predict heterosis. Manipulating heterosis following the strategy based on the prediction is encouraging and very promising with a large number of new knowledge on heterosis being accumulated. Hybrid exhibits heterosis not only in yield but also in adaptation to eco-geographical regions. However compared to yield heterosis, the genetic basis of heterosis in adaptation is less touched and needs to be emphasized in future. Currently, making a proper experimental design for evaluating adaptation is a big challenge because there is no commonly accepted trait to estimate eco-geographical adaptation. Isolation of more heading date genes would probably help us to understand adaptation. Unveiling the molecular mechanism of key yield related genes will better understand the mechanism underlying dominance and overdominance and enhance the efficiency of breeding hybrids with strong heterosis.

Exome sequencing of geographically diverse barley landraces and wild relatives gives insights into environmental adaptation

After domestication, during a process of widespread range extension, barley adapted to a broad spectrum of agricultural environments. To explore how the barley genome responded to the environmental challenges it encountered, we sequenced the exomes of a collection of 267 georeferenced landraces and wild accessions. A combination of genome-wide analyses showed that patterns of variation have been strongly shaped by geography and that variant-by-environment associations for individual genes are prominent in our data set. We observed significant correlations of days to heading (flowering) and height with seasonal temperature and dryness variables in common garden experiments, suggesting that these traits were major drivers of environmental adaptation in the sampled germplasm. A detailed analysis of known flowering-associated genes showed that many contain extensive sequence variation and that patterns of single- and multiple-gene haplotypes exhibit strong geographical structuring. This variation appears to have substantially contributed to range-wide ecogeographical adaptation, but many factors key to regional success remain unidentified.

Combinations of the Ghd7, Ghd8 and Hd1 genes largely define the ecogeographical adaptation and yield potential of cultivated rice.

Rice cultivars have been adapted to favorable ecological regions and cropping seasons. Although several heading date genes have separately made contributions to this adaptation, the roles of gene combinations are still unclear. We employed a map-based cloning approach to isolate a heading date gene, which coordinated the interaction between Ghd7 and Ghd8 to greatly delay rice heading. We resequenced these three genes in a germplasm collection to analyze natural variation. Map-based cloning demonstrated that the gene largely affecting the interaction between Ghd7 and Ghd8 was Hd1. Natural variation analysis showed that a combination of loss-of-function alleles of Ghd7, Ghd8 and Hd1 contributes to the expansion of rice cultivars to higher latitudes; by contrast, a combination of pre-existing strong alleles of Ghd7, Ghd8 and functional Hd1 (referred as SSF) is exclusively found where ancestral Asian cultivars originated. Other combinations have comparatively larger favorable ecological scopes and acceptable grain yield. Our results indicate that the combinations of Ghd7, Ghd8 and Hd1 largely define the ecogeographical adaptation and yield potential in rice cultivars. Breeding varieties with the SSF combination are recommended for tropical regions to fully utilize available energy and light resources and thus produce greater yields.

Genetic structure and eco-geographical adaptation of garlic landraces (Allium sativum L.) in Iran

In this study we present the genetic analysis of freshly collected garlic landraces (Allium sativum L.) along an eco-geographical transect from northeastern to western Iran covering seven different provinces using ISSR and RAPD markers. A total of 52 polymorphic loci were detected among 31 landrace populations. The percentage of polymorphic bands, the mean effective number of alleles, and the mean gene diversity were 38.82 %, 1.54, and 0.32, respectively. Genetic principal co-ordinate analysis and Structure analysis using 52 polymorphic loci indicated that the germplasm could be divided into two major groups. Principal component analysis (PCA), using geographical and environmental variables suggested the role of both geographical and environmental adaptation in driving and maintaining genetic differentiation between the major groups. In addition, our results showed that the combination of latitude, altitude, and precipitation explains the highest proportion of the variance in the PCA of eco-geographical data. This study shows that geographical and environmental factors together created stronger and more discrete genetic differentiation than isolation by distance alone. These findings emphasize the importance of environmental selection in shaping patterns of genetic structure inferred in Iranian garlic germplasm. We suggest that action should be immediately taken for collecting, protecting and evaluating the genetic diversity of garlic landraces before they disappear in Iran.

Genetic structure and ecogeographical adaptation in wild barley (Hordeum chilenseRoemer et Schultes) as revealed by microsatellite markers

BackgroundMulti-allelic microsatellite markers have become the markers of choice for the determination of genetic structure in plants. Synteny across cereals has allowed the cross-species and cross-genera transferability of SSR markers, which constitute a valuable and cost-effective tool for the genetic analysis and marker-assisted introgression of wild related species. Hordeum chilense is one of the wild relatives with a high potential for cereal breeding, due to its high crossability (both interspecies and intergenera) and polymorphism for adaptation traits. In order to analyze the genetic structure and ecogeographical adaptation of this wild species, it is necessary to increase the number of polymorphic markers currently available for the species. In this work, the possibility of using syntenic wheat SSRs as a new source of markers for this purpose has been explored.ResultsFrom the 98 wheat EST-SSR markers tested for transferability and polymorphism in the wild barley genome, 53 primer pairs (54.0%) gave cross-species transferability and 20 primer pairs (20.4%) showed polymorphism. The latter were used for further analysis in the H. chilense germplasm. The H. chilense-Triticum aestivum addition lines were used to test the chromosomal location of the new polymorphic microsatellite markers. The genetic structure and diversity was investigated in a collection of 94 H. chilense accessions, using a set of 49 SSR markers distributed across the seven chromosomes. Microsatellite markers showed a total of 351 alleles over all loci. The number of alleles per locus ranged from two to 27, with a mean of 7.2 alleles per locus and a mean Polymorphic Information Content (PIC) of 0.5.ConclusionsAccording to the results, the germplasm can be divided into two groups, with morphological and ecophysiological characteristics being key determinants of the population structure. Geographic and ecological structuring was also revealed in the analyzed germplasm. A significant correlation between geographical and genetic distance was detected in the Central Chilean region for the first time in the species. In addition, significant ecological influence in genetic distance has been detected for one of the population structure groups (group II) in the Central Chilean region. Finally, the association of the SSR markers with ecogeographical variables was investigated and one marker was found significantly associated with precipitation. These findings have a potential application in cereal breeding.

Horizontal, Technical Cooperation in Research on Quinoa (Chenopodium quinoaWilld.)

Quinoa possesses remarkable characteristics in terms of its productive potential and eco-geographical adaptation (0 to 4000 msnm; 200 to 1000 mm of rainfall; −1 to 35°C, and short to (neutral) photoperiod). The market potential is large, and quinoa is already known in the United States, Canada, Europe, and Asia, as a basic source of protein of high biological value. FAO has suggested the crop be included as a source for food security in the next century (FAO, [1998]) Bolivia and Peru are the major producers of quinoa, with 70000 ha under cultivation.