Heterosis in the freezing tolerance, and sugar and flavonoid contents of crosses between Arabidopsis thaliana accessions of widely varying freezing tolerance

Heterosis is defined as the increased vigour of hybrids in comparison to their parents. We investigated 24 F(1) hybrid lines of Arabidopsis thaliana generated by reciprocally crossing either C24 or Col with six other parental accessions (Can, Co, Cvi, Ler, Rsch, Te) that differ widely in their freezing tolerance. The crosses differed in the degree of heterosis for freezing tolerance, both in the non-acclimated state and after a 14 d cold acclimation period. Crosses with C24 showed more heterosis than crosses with Col, and heterosis was stronger in acclimated than in non-acclimated plants. Leaf content of soluble sugars and proline showed more deviation from mid-parent values in crosses involving C24 than in those involving Col, and deviations were larger in acclimated than in non-acclimated plants. There were significant correlations between the content of different sugars and leaf freezing tolerance, as well as between heterosis effects in freezing tolerance and sugar content. Flavonoid content and composition varied between accessions, and between non-acclimated and acclimated plants. In the crosses, large deviations from the mid-parent values in the contents of different flavonols occurred, and there were strikingly strong correlations between both flavonol content and freezing tolerance, and between heterosis effects in freezing tolerance and flavonol content.     

Comparative analysis on the genetic relatedness of Sorghum bicolor accessions from Southern Africa by RAPDs,AFLPs and SSRs

In order to get an overview on the genetic relatedness of sorghum (Sorghum bicolor) landraces and cultivars grown in low-input conditions of small-scale farming systems, 46 sorghum accessions derived from Southern Africa were evaluated on the basis of amplified fragment length polymorphism (AFLPs), random amplified polymorphic DNAs (RAPDs) and simple sequence repeats (SSRs). By this approach all sorghum accessions were uniquely fingerprinted by all marker systems. Mean genetic similarity was estimated at 0.88 based on RAPDs, 0.85 using AFLPs and 0.31 based on SSRs. In addition to this, genetic distance based on SSR data was estimated at 57 according to a stepwise mutation model (Deltamu-SSR). All UPGMA-clusters showed a good fit to the similarity estimates (AFLPs: r = 0.92; RAPDs: r = 0.88; SSRs: r = 0.87; Deltamu-SSRs: r = 0.85). By UPGMA-clustering two main clusters were built on all marker systems comprising landraces on the one hand and newly developed varieties on the other hand. Further sub-groupings were not unequivocal. Genetic diversity (H, DI) was estimated on a similar level within landraces and breeding varieties. Comparing the three approaches to each other, RAPD and AFLP similarity indices were highly correlated (r = 0.81), while the Spearman's rank correlation coefficient between SSRs and AFLPs was r = 0.57 and r = 0.51 between RAPDs and SSRs. Applying a stepwise mutation model on the SSR data resulted in an intermediate correlation coefficient between Deltamu-SSRs and AFLPs (r = 0.66) and RAPDs ( r = 0.67), respectively, while SSRs and Deltamu-SSRs showed a lower correlation coefficient (r = 0.52). The highest bootstrap probabilities were found using AFLPs (56% on average) while SSR, Deltamu-SSR and RAPD-based similarity estimates had low mean bootstrap probabilities (24%, 27%, 30%, respectively). The coefficient of variation (CV) of the estimated genetic similarity decreased with an increasing number of bands and was lowest using AFLPs.     

Direct comparison of levels of genetic variation among barley accessions detected by RFLPs, AFLPs, SSRs and RAPDs

 RFLPs, AFLPs, RAPDs and SSRs were used to determine the genetic relationships among 18 cultivated barley accessions and the results compared to pedigree relationships where these were available. All of the approaches were able to uniquely fingerprint each of the accessions. The four assays differed in the amount of polymorphism detected. For example, all 13 SSR primers were polymorphic, with an average of 5.7 alleles per primer set, while nearly 54% of the fragments generated using AFLPs were monomorphic. The highest diversity index was observed for AFLPs (0.937) and the lowest for RFLP (0.322). Principal co-ordinate analysis (PCoA) clearly separated the spring types from the winter types using RFLP and AFLP data with the two-row winter types forming an intermediate group. Only a small group of spring types clustered together using SSR data with the two-row and six-row winter varieties more widely dispersed. Direct comparisons between genetic similarity (GS) estimates revealed by each of the assays were measured by a number of approaches. Spearman rank correlation ranked over 70% of the pairwise comparisons between AFLPs and RFLPs in the same order. SSRs had the lowest values when compared to the other three assays. These results are discussed in terms of the choice of appropriate technology for different aspects of germplasm evaluation.     

GBS-SNP and SSR based genetic mapping and QTL analysis for drought tolerance in upland cotton

A recombinant inbred line mapping population of intra-species upland cotton was generated from a cross between the drought-tolerant female parent (AS2) and the susceptible male parent (MCU13). A linkage map was constructed deploying 1,116 GBS-based SNPs and public domain-based 782 SSRs spanning a total genetic distance of 28,083.03 cM with an average chromosomal span length of 1,080.12 cM with inter-marker distance of 10.19 cM.A total of 19 quantitative trait loci (QTLs) were identified in nine chromosomes for field drought tolerance traits. Chromosomes 3 and 8 harbored important drought tolerant QTLs for chlorophyll stability index trait while for relative water content trait, three QTLs on chromosome 8 and one QTL each on chromosome 4, 12 were identified. One QTL on each chromosome 8, 5, and 7, and two QTLs on chromosome 15 linking to proline content were identified. For the nitrate reductase activity trait, two QTLs were identified on chromosome 3 and one on each chromosome 8, 13, and 26. To complement our QTL study, a meta-analysis was conducted along with the public domain database and resulted in a consensus map for chromosome 8. Under field drought stress, chromosome 8 harbored a drought tolerance QTL hotspot with two in-house QTLs for chlorophyll stability index (qCSI01, qCSI02) and three public domain QTLs (qLP.FDT_1, qLP.FDT_2, qCC.ST_3). Identified QTL hotspot on chromosome 8 could play a crucial role in exploring abiotic stress-associated genes/alleles for drought trait improvement.Supplementary InformationThe online version contains supplementary material available at 10.1007/s12298-021-01041-y.     

Estimation of genetic variation in Cynodon dactylon accessions using the ISSR technique

Genetic variation in 55 accessions of Cynodon dactylon was estimated using inter-simple sequence repeat (ISSR) markers. The plant materials used in this study originated from 17 countries. A total of 236 ISSR fragments were generated with 14 primers. Fragment sizes ranged from 200 to 3000 bp. All scorable bands were polymorphic in nature and none of the primers used produced monomorphic bands, indicating a high level of genetic variation in this grass. The accessions were found to be clustered into eight major groups through the unweighted pair-group method with arithmetic averages. Genetic similarity coefficients (GSC) among the 55 accessions ranged from 0.52 to 0.95. The results clearly indicate that a high level of variation exists in Cynodon accessions. This study shows that the ISSR technique is a reliable tool for differentiating Cynodon accessions and for determining the genetic relationships among them.     

兰属14种植物遗传多样性RAPD及AFLP分析

用RAPD和AFIJP技术分析了14种兰属植物的遗传多样性。RAPD筛选出12个随机引物和AFLP3对选择性引物组合均扩增出了丰富的多态性片段。分析结果按UPGMA类平均法进行聚类,所得到的RAPD和AFLP聚类结果基本一致,显示建兰与墨兰,寒兰与峨眉春蕙以及大雪兰与独占春之间的亲缘关系最近。     

Estimation of evolutionary distance between nucleotide sequences

A mathematical formula for estimating the average number of nucleotide substitutions per site (delta) between two homologous DNA sequences is developed by taking into account unequal rates of substitution among different nucleotide pairs. Although this formula is obtained for the equal-input model of nucleotide substitution, computer simulations have shown that it gives a reasonably good estimate for a wide range of nucleotide substitution patterns as long as delta is equal to or smaller than 1. Furthermore, the frequency of cases to which the formula is inapplicable is much lower than that for other similar methods recently proposed. This point is illustrated using insulin genes. A statistical method for estimating the number of nucleotide changes due to deletion and insertion is also developed. Application of this method to globin gene data indicates that the number of nucleotide changes per site increases with evolutionary time but the pattern of the increase is quite irregular.      

Assessment of genetic diversity in Colletotrichum falcatum Went accessions based on RAPD and ISSR markers

Sugarcane is susceptible to red rot disease caused by phytopathogenic fungus Colletotrichum falcatum Went which ultimately affect the economy of farmers as well as sugar based industry. One of the various ways to control this devastating disease is to develop disease resistance sugarcane cultivar and this requires the complete understanding of genetic makeup of pathogen. Although South Gujarat is well known sugarcane cultivating area, less published data can be found about PCR-based genetic diversity in prevalent C. falcatum accessions. So, present investigation aims at finding molecular variation among the ten accessions of C. falcatum using RAPD and ISSR molecular markers. A total of 35 RAPD and 39 ISSR primers were screened across 10 C. falcatum accessions, of which 15 RAPD and 21 ISSR primers have showed consistent amplification. Statistics related to genetic variation were estimated using NTSYS-PC by means of Dice’s coefficient. The results revealed 80.6% and 68.07% polymorphism and similarity coefficient ranged from 0.43 to 0.91 and 0.73 to 0.93 in RPAD and ISSR analysis respectively. The dendrogram generated using RAPD, ISSR and combined RAPD-ISSR grouped accessions into different clusters which reveal considerable level molecular variation among the C. falcatum accessions. It is also evident from PCA plots that accessions are rather dispersed with tested marker systems indicating good genetic base. So, in nut shell, we found considerable genetic variation and relatedness within C. falcatum accessions collected from different areas of south Gujarat, India using RAPD and ISSR markers.     

基于冠层反射光谱的棉花叶片氮含量估测

通过分析不同施氮水平下棉花叶片氮含量与冠层多光谱反射率及其衍生的比值、归一化及差值植被指数之间的关系,确立了棉花叶片氮含量的敏感波段及预测方程.结果表明:由红谷区域(610、660、680和710nm4个波段)和近红外区域(760、810、870、950、1100和1220nm6个波段)组成的植被指数与棉花叶片氮含量的相关性较好,比值植被指数RVI(950,710)对叶片氮含量的预测性最好.利用独立的棉花田间试验资料对基于RVI(950,710)的预测方程进行检验,该模型适用于不同棉花品种及不同生育期棉花叶片氮含量预测.     

Okra-leaf accessions of the upland cotton (Gossypium hirsutum L.): genetic variability in agronomic and fibre traits

Okra-leaf types of the upland cotton have the potential to be competitive to the normal-leaf types in yield and fibre quality, in addition to its potential resistance to insect pests and drought. Okra-leaf cotton accessions, collected at Cotton Research Institute, Faisalabad, Pakistan, were evaluated in respect of genetic variance and relative performance in half- and full-sib crosses (combining ability) for 2 years. Variation due to parents x years interaction was significant for lint percentage, seed weight and earliness index, resulting in moderately low but significant genetic variance across environments (years) for these traits. Interaction of environment with general combining ability was significant for seed yield, seed weight, and earliness index. General combining ability variation, contributed by females and males together, accounted for 71% of the total variation available for seed cotton yield, 60% of that for seed weight and height to node ratio each, and 75% of that for earliness index. Specific combining ability variation accounted for 85% and 51% of the total variation available for lint percentage and staple length, respectively. The contribution of female parents to general combining ability variation was higher than that of male parents for seed cotton yield, seed weight, height to node ratio, and earliness index. Okra-leaf accessions HR-VO-MS and HR107-NH were predicted to produce progenies having high yield, HR109-RT high lint percentage, while HR100-Okra, Gambo-Okra and HR-VO-1 were predicted to impart early crop maturity to their progenies by reason of their good general combining ability for these traits. The results also provided evidence that genes controlling high yield in HR-VO-MS and HR107-NH were different from those controlling high yield in HR109-RT. The set of genes controlling the high earliness index in HR100-Okra and that in HR-VO-MS also appeared to differ in expression.     

Estimation of the coancestry coefficient: basis for a short-term genetic distance

A distance measure for populations diverging by drift only is based on the coancestry coefficient θ, and three estimators of the distance D = -ln(1 - θ) are constructed for multiallelic, multilocus data. Simulations of a monoecious population mating at random showed that a weighted ratio of single-locus estimators performed better than an unweighted average or a least squares estimator. Jackknifing over loci provided satisfactory variance estimates of distance values. In the drift situation, in which mutation is excluded, the weighted estimator of D appears to be a better measure of distance than others that have appeared in the literature.     

Anthropometric and genetic distance between Gonds of Central India

A morphological and genetic study was undertaken on five Gondi-speaking populations of Central India (Andhra Pradesh and Maharashtra States). There has been no systematic biological study on this large Dravidian-speaking tribal group, 4 million in number, amounting to 13% of the total tribal population of India. Data was collected on 16 anthropometric measurements and seven genetic markers (blood groups, hemoglobin, G6PD and plasma protein polymorphisms) on the Raj Gonds, Kolams, Manne, Koyas and Plains Maria Gonds. Various genetic distance measures such as Mahalanobis's D2 and Nei's and Sanghvi's measures and cluster analysis techniques were used to determine the relationship between these groups based on anthropometrics and genetic variables. The statistical analysis revealed the Gonds to be a heterogenous group in both morphology and genetic characteristics. The morphological and genetic distances between these five groups when projected graphically revealed that the spatial distribution of these Gonds generally corresponds to their present geographical distribution. However, the actual relationships among each of the Gond populations show differences when based on these two biological variables, the possible reasons for this being discussed in the paper. The emphasis of this study is on the importance of geographical proximity in producing morphological and genetic similarity between populations, brought about by a short distance as well as similar geographical factors (such as soil, terrain, flora, etc.) drawing these populations together under a common ecocultural umbrella.     

Estimation of genetic diversity in some Iranian cornelian cherries (Cornus mas L.) accessions using ISSR markers

Iran is an important producer of cornelian cherries (Cornus mas L.). Seed propagation and long term human selection have given rise to a great diversity of trees. In this study, ISSR marker was used for genetic diversity evaluation of 40 accessions of cornelian cherries (C. mas L.). With 20 ISSR primers, 171 polymorphic bands were detected with polymorphism ratio range of 80–100%. The average polymorphism information content (PIC) was 0.46, which shows that the majority of primers are informative. The average values of Effective Multiplex Ratio (EMR), Marker Index (MI), effective number of alleles (Ne), Nei's gene diversity (He) and Shannon's information index (I) for all primers were 8.0, 3.75, 1.756, 0.416 and 0.595 respectively. Based on these results, ISSR analysis can be used for the characterization and grouping of cornelian cherry accessions. This is the first study demonstrating that ISSR analyses can be used to differentiate and classify cornelian cherry accessions.     

Genetic diversity of Picea asperata populations based on RAPDs

The genetic diversity of ten natural populations of Picea asperata Mast. were studied using RAPD markers. A total of 160 reproducible fragments were produced from the ten primers used. The mean number of fragments detected per individual was 114.7. Altogether 120 fragments were polymorphic among the ten populations, none of them were found to be population-specific. Nei's expected heterozygosity (H (e)) ranged from 0.233 to 0.269, and the average was 0.247. The analysis of molecular variance revealed that the coefficient of gene differentiation among populations, based on F (ST) and the unbiased estimate PhiST, equaled 0.224 and 0.290, respectively. Such high values indicate that there is significant differentiation among populations, which could result from several factors, including restricted gene flow between populations (Nm = 0.866). Founder events may be another factor attributing to the high level of genetic differentiation. In addition, it was discovered that the geographic distribution is not correlated with the genetic distances among the populations of P. asperata.     

Estimation of average heterozygosity and genetic distance from a small number of individuals

The magnitudes of the systematic biases involved in sample heterozygosity and sample genetic distances are evaluated, and formulae for obtaining unbiased estimates of average heterozygosity and genetic distance are developed. It is also shown that the number of individuals to be used for estimating average heterozygosity can be very small if a large number of loci are studied and the average heterozygosity is low. The number of individuals to be used for estimating genetic distance can also be very small if the genetic distance is large and the average heterozygosity of the two species compared is low.     

Proteomics of rice in response to heat stress and advances in genetic engineering for heat tolerance in rice

Rice is the most important food crop worldwide. Global warming inevitably affects the grain yields of rice. Recent proteomics studies in rice have provided evidence for better understanding the mechanisms of thermal adaptation. Heat stress response in rice is complicated, involving up- or down-regulation of numerous proteins related to different metabolic pathways. The heat-responsive proteins mainly include protection proteins, proteins involved in protein biosynthesis, protein degradation, energy and carbohydrate metabolism, and redox homeostasis. In addition, increased thermotolerance in transgenic rice was obtained by overexpression of rice genes and genes from other plants. On the other hand, heterologous expression of some rice proteins led to enhanced thermotolerance in bacteria and other easily transformed plants. In this paper, we review the proteomic characterization of rice in response to high temperature and achievements of genetic engineering for heat tolerance in rice.     

Global patterns of isolation by distance based on genetic and morphological data

The isolation-by-distance model predicts that genetic similarity between populations will decrease exponentially as the geographic distance between them increases, because of the limiting effect of geographic distance on rates of gene flow. Many studies of human populations have applied the isolation-by-distance model to genetic variation between local populations in a limited geographic area, but few have done so on a global level, and these few used different models and analytical methods. I assess genetic variation between human populations across the world using data on red blood cell polymorphisms, microsatellite DNA markers, and craniometric traits. The isolation-by-distance model provides an excellent fit to average levels of genetic similarity within geographic distance classes for all three data sets, and the rate of distance decay is the same in all three. These results suggest that a common pattern of global gene flow mediated by geographic distance is detectable in diverse genetic and morphological data. An alternative explanation is that the correspondence between genetic similarity and geographic distance reflects the history of dispersal of the human species out of Africa.     

Studies on heat tolerance at rest and orthostatic heat tolerance in a hot environment

Twelve young male Japanese were exposed to a hot environment in summer, and changes in systolic blood pressure induced by changing the position from recumbent to sitting were observed. Sweating was induced in a climatic chamber at 30 degree C with 70% relative humidity by immersing both legs up to the knees into a water bath of 42 degree C for 90 min after sitting on a chair at rest for 30 min in the chamber. The mean values of rise in rectal temperature, body weight loss and mean sodium concentration in sweat were 0.62 degree C, 0.67 kg and 46 mEq/l, respectively. The mean values of fall in systolic blood pressure associated with changing posture and its recovery time were 13.7 mm Hg and 77.5 sec, respectively. Heat tolerance at rest was assessed by a numerical heat tolerance index involving relative water loss, relative rise in rectal temperature, and relative salt loss. Values of relative water loss, relative rise in rectal temperature, and the numerical heat tolerance index correlated closely to those of fall in systolic blood pressure and its recovery time.