Screening of rice (Oryza sativa L.) genotypes for physiological characters contributing to salinity resistance,and their relationship to overall performance

Summary Phenotypic resistance of salinity is expressed as the ability to survive and grow in a salinised medium. Some subjective measure of overall performance has normally been used in plant breeding programmes aimed at increasing salinity resistance, not only to evaluate progeny, but to select parents. Salinity resistance has, at least implicitly, been treated as a single trait. Physiological studies of rice suggest that a range of characteristics (such as low shoot sodium concentration, compartmentation of salt in older rather than younger leaves, tolerance to salt within leaves and plant vigour) would increase the ability of the plant to cope with salinity. We describe the screening of a large number of rice genotypes for overall performance (using an objective measure based on survival) and for the aforementioned physiological traits. There was wide variation in all the characters studied, but only vigour was strongly correlated with survival. Shoot sodium concentration, which a priori is expected to be important, accounted for only a small proportion of the variability in the survival of salinity. Tissue tolerance (the cellular component of resistance reflecting the ability to compartmentalise salt within leaves) revealed a fivefold range between genotypes in the tolerance of their leaves to salt, but this was not correlated positively with survival. On the basis of such (lack of) correlation, these traits would be rejected in normal plant breeding practice, but we discuss the fallacies involved in attempting correlation between individual traits and the overall performance of a salt-sensitive species in saline conditions. We conclude that whilst overall performance (survival) can be used to evaluate the salt resistance of a genotype, it is not the basis on which parents should be selected to construct a complex character through breeding. It was the norm for varieties which had one good characteristic affecting salt resistance to be unexceptional or poor in the others. This constitutes experimental evidence that the potential for salt resistance present in the rice genome has not been realised in genotypes currently extant. The results are discussed in relation to the use of physiological traits in plant breeding, with particular reference to environmental stresses that do not affect a significant part of a species' ecological range.     

Genomic screening for artificial selection during domestication and improvement in maize

BACKGROUND: Artificial selection results in phenotypic evolution. Maize (Zea mays L. ssp. mays) was domesticated from its wild progenitor teosinte (Zea mays subspecies parviglumis) through a single domestication event in southern Mexico between 6000 and 9000 years ago. This domestication event resulted in the original maize landrace varieties. The landraces provided the genetic material for modern plant breeders to select improved varieties and inbred lines by enhancing traits controlling agricultural productivity and performance. Artificial selection during domestication and crop improvement involved selection of specific alleles at genes controlling key morphological and agronomic traits, resulting in reduced genetic diversity relative to unselected genes. SCOPE: This review is a summary of research on the identification and characterization by population genetics approaches of genes affected by artificial selection in maize. CONCLUSIONS: Analysis of DNA sequence diversity at a large number of genes in a sample of teosintes and maize inbred lines indicated that approx. 2 % of maize genes exhibit evidence of artificial selection. The remaining genes give evidence of a population bottleneck associated with domestication and crop improvement. In a second study to efficiently identify selected genes, the genes with zero sequence diversity in maize inbreds were chosen as potential targets of selection and sequenced in diverse maize landraces and teosintes, resulting in about half of candidate genes exhibiting evidence for artificial selection. Extended gene sequencing demonstrated a low false-positive rate in the approach. The selected genes have functions consistent with agronomic selection for plant growth, nutritional quality and maturity. Large-scale screening for artificial selection allows identification of genes of potential agronomic importance even when gene function and the phenotype of interest are unknown. These approaches should also be applicable to other domesticated species if specific demographic conditions during domestication exist.     

The genetics of adaptation to novel environments: selection on germination timing in Arabidopsis thaliana

When studying selection during adaptation to novel environments, researchers have often paid little attention to an organism’s earliest developmental stages. Despite this lack of attention, early life history traits may be under strong selection during colonization, as the expression of adaptive phenotypes at later points is contingent upon early survival. Moreover, the timing of early developmental transitions can constrain the timing of later transitions, with potentially large effects on fitness. In this issue, Huang et al. (2010) underscore the importance of early life history traits in the adaptation of Arabidopsis thaliana to old‐field sites in North America. Using a new population of mapped recombinant inbred lines, the authors examined germination timing and total lifetime fitness of A. thaliana while varying site latitude, dispersal season, and maternal photoperiod. Huang et al. (2010) discovered several Quantitative Trait Loci (QTL) with large effects on fitness that colocalized with QTL for field germination timing and seed dormancy—demonstrating that fitness is genetically associated with these early life history traits, and that these loci are likely under strong selection during adaptation to novel environments. In the epistatic interactions of some loci, recombinant genotypes outperformed parental genotypes, supporting the potentially adaptive role of recombination. This study provides elegant evidence that traits expressed early in an organism’s development can play an important role during adaptive evolution.     

A Study on Genotype-by-Environment Interaction Analysis for Agronomic Traits of Maize Genotypes Across Huang-Huai-Hai Region in China

Facing the trend of increasing population, how to increase maize grain yield is a very important issue to ensure food security. In this study, 28 nationally approved maize hybrids were evaluated across 24 different climatic conditions for two consecutive years (2018–2019). The purpose of this study was to select high-yield with stable genotypes and identify important agronomic traits for maize breeding program improvement. The results of this study showed that the genotype ╳ environment interaction effects of the 12 evaluated agronomic traits was highly significant (P < 0.001). We introduced a novel multi-trait genotype-ideotype distance index (MGIDI) to select genotypes based on multiple agronomic traits. The selection process exhibited by this method is unique and easy to understand, so the MGIDI index will have more and more important applications in future multi-environment trials (METs) research. The genotypes selected by the MGIDI index were G22, G10, G12 and G1 as the high yielding and stable genotypes. The parents of these selected genotypes have the ability to play a greater role as the basic germplasm in the breeding process. A new form of genotype (G) main effects and genotype (G) -by-environment (E) interaction (GGE) technician, genotype*yield*trait (GYT) biplot, based on multiple traits for genotypes selection was also applied in this study. The GYT biplot ranked genotypes by combining grain yield with other evaluated agronomic traits, and displayed the distribution of their traits, namely strengths and weaknesses.     

Choice of selection environment for improving crop yields in saline areas

Spatial variability in salt-affected fields is normally very high. Thus, most salinity affected lands are actually comprised of many micro-environments, ranging from low to high salinity in the same field. The evidence on testing genotypes across a broad range of salinity levels shows that the genotype-by-salinity level interaction is commonly large. Thus, breeding for saline areas can be compared to what has been known as breeding for wide adaptation. The target environments both for breeding for saline soils or for wide adaptation are actually a population of many possible environments, for which there exists a significant component of genotype-by-environment(G x E) interaction. Thus it is possible to study the merit of potential strategies for breeding for salinity tolerance using the tools that have been developed for the study of breeding for wide adaptation. The evidence from selection and breeding experiments for wide adaptation seems to favour testing on a representative subset of environments, including stress and non-stress locations; but the choice of these locations is complicated by the multidimensional nature of G x E. However, in the case of salt stress, the crop-yield response functions to salinity are well known. This paper presents an attempt to systematise the choice of the optimum environment(s) to select for improved yield under saline soil conditions, based on the three-piece linear equation presented by Maas and Hoffman (1977) and the theory of direct and indirect responses to selection. It is proposed that three saline levels should be enough to make a valid estimation of the suitability of a number of selection strategies. A worked example with data from a set of grain sorghum inbred lines tested on ten saline levels shows that the same selection strategies would be chosen using the information from the ten saline levels as that obtained using the two extremes and one intermediate level.     

Direct and correlated responses to selection for longevity in Drosophila buzzatii

The possible associations between longevity, early fecundity, and stress-resistance traits were explored using artificial selection on longevity in a laboratory population of Drosophila buzzatii . Three replicated lines were selected for increased lifespan (L lines) and compared with the respective unselected controls (C lines) after the 14th generation of selection. Mean longevity exhibited a significant response to selection. The baseline mortality tended to decrease in the L lines and a negative correlated response to longevity selection was found for early fecundity. Egg-to-adult developmental time increased in L lines. Longevity selection increased stress resistance for both high and low temperatures, as measured by heat knockdown resistance and chill-coma recovery. Starvation resistance also tended to be higher in L than in C lines. The results obtained are consistent with the hypothesis of trade-offs between longevity and early fecundity, and also suggest a trade-off association between adult longevity and developmental time. Correlated selection responses were generally consistent with correlations among the traits previously inferred from altitudinal clines for longevity and stress-resistance phenotypes.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 97 , 738–748.     

Quantitative trait loci (QTL) mapping for physiological and biochemical attributes in a Pasban90/Frontana recombinant inbred lines (RILs) population of wheat (Triticum aestivum) under salt stress condition

Salt stress causes nutritional imbalance and ion toxicity which affects wheat growth and production. A population of recombinant inbred lines (RILs) were developed by crossing Pasban90 (salt tolerant) and Frontana (salt suceptible) for identification of quantitative trait loci (QTLs) for physiological traits including relative water content, membrane stability index, water potential, osmotic potential, total chlorophyll content, chlorophyll a, chlorophyll b and biochemical traits including proline contents, superoxide dismutase, sodium content, potassium content, chloride content and sodium/potassium ratio by tagging 202 polymorphic simple sequence repeats (SSR) markers. Linkage map of RILs comprised of 21 linkage group covering A, B and D genome for tagging and maped a total of 60 QTLs with major and minor effect. B genome contributed to the highest number of QTLs under salt stress condition. Xgwm70 and Xbarc361 mapped on chromosome 6B was linked with Total chlorophyll, water potential and sodium content. The increasing allele for all these QTLs were advanced from parent Pasban90. Current study showed that Genome B and D had more potentially active genes conferring plant tolerance against salinity stress which may be exploited for marker assisted selection to breed salinity tolerant high yielding wheat varieties.     

Quantitative trait loci for component physiological traits determining salt tolerance in rice

Rice (Oryza sativa) is sensitive to salinity, which affects one-fifth of irrigated land worldwide. Reducing sodium and chloride uptake into rice while maintaining potassium uptake are characteristics that would aid growth under saline conditions. We describe genetic determinants of the net quantity of ions transported to the shoot, clearly distinguishing between quantitative trait loci (QTL) for the quantity of ions in a shoot and for those that affect the concentration of an ion in the shoot. The latter coincide with QTL for vegetative growth (vigor) and their interpretation is therefore ambiguous. We distinguished those QTL that are independent of vigor and thus directly indicate quantitative variation in the underlying mechanisms of ion uptake. These QTL independently govern sodium uptake, potassium uptake, and sodium:potassium selectivity. The QTL for sodium and potassium uptake are on different linkage groups (chromosomes). This is consistent with the independent inheritance of sodium and potassium uptake in the mapping population and with the mechanistically different uptake pathways for sodium and potassium in rice under saline conditions (apoplastic leakage and membrane transport, respectively). We report the chromosomal location of ion transport and selectivity traits that are compatible with agronomic needs and we indicate markers to assist selection in a breeding program. Based upon knowledge of the underlying mechanisms of ion uptake in rice, we argue that QTL for sodium transport are likely to act through the control of root development, whereas QTL for potassium uptake are likely to act through the structure or regulation of membrane-sited transport components.     

Assessing the correlations and selection criteria between different traits in wheat salt-tolerant genotypes

Salinity is one of the largest stresses blocking horizontal and vertical expansion in agricultural lands. Establishing salt-tolerant genotypes is a promising method to benefit from poor water quality and salinized lands. An integrated method was developed for accomplishing reliable and effective evaluation of traits stability of salt-tolerant wheat. The study aims were to estimate the genetic relationships between explanatory traits and shoot dry matter (SDM), and determine the traits stability under three salinity levels. Morphophysiological and biochemical traits were evaluated as selection criteria for SDM improvement in wheat for salinity tolerance. Three cultivars and three high-yielding doubled haploid lines (DHLs) were used. Three salt (NaCl) levels (control (washed sand), 7 and 14 dS m⁻¹) were applied for 45 days (at the first signs of death in the sensitive genotypes). All morphophysiological traits gradually decreased as salinity levels increased, excluding the number of roots. Decreases were more visible in sensitive genotypes than in tolerant genotypes. All biochemical traits increased as salinity levels increased. Variance inflation factors (VIFs) and condition number exhibited multicollinearity for membrane stability index and polyphenol oxidase activity. After their removal, all VIFs were <10, thereby increasing path coefficient accuracy. Total chlorophyll content (CHL) and catalase (CAT) provided significant direct effects regarding genetic and phenotypic correlations for the three salinity levels and their interactions in path analysis on SDM, indicating their stability. CHL and CAT had high heritability (>0.60%) and genetic gain (>20%) and highly significant genetic correlation, co-heritability, and selection efficiencies for SDM. CHL and CAT could be used as selection criteria for salinity tolerance in wheat-breeding programs. The tolerated line (DHL21) with the check cultivar (Sakha 93) can be also recommended as novel genetic resource for improving salinity tolerance of wheat.     

Genomic consequences of selection and genome-wide association mapping in soybean

Background

Crop improvement always involves selection of specific alleles at genes controlling traits of agronomic importance, likely resulting in detectable signatures of selection within the genome of modern soybean (Glycine max L. Merr.). The identification of these signatures of selection is meaningful from the perspective of evolutionary biology and for uncovering the genetic architecture of agronomic traits.

Results

To this end, two populations of soybean, consisting of 342 landraces and 1062 improved lines, were genotyped with the SoySNP50K Illumina BeadChip containing 52,041 single nucleotide polymorphisms (SNPs), and systematically phenotyped for 9 agronomic traits. A cross-population composite likelihood ratio (XP-CLR) method was used to screen the signals of selective sweeps. A total of 125 candidate selection regions were identified, many of which harbored genes potentially involved in crop improvement. To further investigate whether these candidate regions were in fact enriched for genes affected by selection, genome-wide association studies (GWAS) were conducted on 7 selection traits targeted in soybean breeding (grain yield, plant height, lodging, maturity date, seed coat color, seed protein and oil content) and 2 non-selection traits (pubescence and flower color). Major genomic regions associated with selection traits overlapped with candidate selection regions, whereas no overlap of this kind occurred for the non-selection traits, suggesting that the selection sweeps identified are associated with traits of agronomic importance. Multiple novel loci and refined map locations of known loci related to these traits were also identified.

Conclusions

These findings illustrate that comparative genomic analyses, especially when combined with GWAS, are a promising approach to dissect the genetic architecture of complex traits.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1872-y) contains supplementary material, which is available to authorized users.     

Novel screening protocol for precise phenotyping of salt-tolerance at reproductive stage in rice

The present study reports an unequivocal and improved protocol for efficient screening of salt tolerance at flowering stage in rice, which can aid phenotyping of population for subsequent identification of QTLs associated with salinity stress, particularly at reproductive stage. To validate the new method, the selection criteria, level and time of imposition of stress; plant growth medium were standardized using three rice genotypes. The setup was established with a piezometer placed in a perforated pot for continuous monitoring of soil EC and pH throughout the period of study. Further, fertilizer enriched soil was partially substituted by gravels for stabilization and maintaining the uniformity of soil EC in pots without hindering its buffering capacity. The protocol including modified medium (Soil:Stone, 4:1) at 8 dS m^?1 salinity level was validated using seven different genotypes possessing differential salt sensitivity. Based on the important selection traits such as high stability index for plant yield, harvest index and number of grains/panicle and also high K⁺ concentration and low Na⁺– K⁺ ratio in flag leaf at grain filling stage were validated and employed in the evaluation of a mapping population in the modified screening medium. The method was found significantly efficient for easy maintenance of desired level of soil salinity and identification of genotypes tolerant to salinity at reproductive stage.     

Molecular marker-assisted selection for malting quality traits in barley

Selection for malting quality in breeding programs by micromalting and micromashing is time-consuming, and resource-intensive. More efficient and feasible approaches for identifying genotypes with good malting quality would be highly desirable. With the advent of molecular markers, it is possible to map and tag the loci affecting malting quality. The objective of this study was to assess the effectiveness of molecular marker assisted selection for malting quality traits. Two major quantitative trait loci (QTL) regions in six-row barley for malt extract percentage, -amylase activity, diastatic power, and malt -glucan content on chromosomes 1 (QTL1) and 4 (QTL2) have been previously identified. The flanking markers, Brz and Amy2, and WG622 and BCD402B, for these two major QTL regions were used in marker-assisted selection. Four alternative selection strategies; phenotypic selection, genotypic selection, tandem genotypic and phenotypic selection, and combined phenotypic and genotypic selection, were compared for both single and multiple trait selection in a population consisting of 92 doubled haploid lines derived from Steptoe × Morex crosses. Marker assisted selection for QTL1 (tandem genotypic and phenotypic selection, and combined phenotypic and genotypic selection) was more effective than phenotypic selection, but for QTL2 was not as effective as phenotypic selection due to a lack of QTL2 effects in the selection population. The effectiveness of tandem genotypic and phenotypic selection makes marker assisted selection practical for traits which are extremely difficult or expensive to measure such as most malting quality traits. It can substantially eliminate undesirable genotypes by early genotyping and keeping only desirable genotypes for later phenotypic selection.     

Simultaneous marker-assisted selection for multiple traits in autogamous crops

A method is presented for the selection of parents with the aim of obtaining improved genotypes in the progeny of a cross. The procedure is designed to select in several unrelated traits simultaneously and is based on the selection of molecular markers that are linked to QTLs. The method was compared with conventional phenotypic selection in simulation experiments for a number of genetic structures underlying the traits and several types of parental populations. Although the method in general provides good results, some of the underlying assumptions may be violated quite easily, thereby reducing the applicability of the procedure in practice. Received: 10 September 1999 / Accepted: 24 August 2000     

Experimental evidence for multivariate stabilizing sexual selection

Stabilizing selection is a fundamental concept in evolutionary biology. In the presence of a single intermediate optimum phenotype (fitness peak) on the fitness surface, stabilizing selection should cause the population to evolve toward such a peak. This prediction has seldom been tested, particularly for suites of correlated traits. The lack of tests for an evolutionary match between population means and adaptive peaks may be due, at least in part, to problems associated with empirically detecting multivariate stabilizing selection and with testing whether population means are at the peak of multivariate fitness surfaces. Here we show how canonical analysis of the fitness surface, combined with the estimation of confidence regions for stationary points on quadratic response surfaces, may be used to define multivariate stabilizing selection on a suite of traits and to establish whether natural populations reside on the multivariate peak. We manufactured artificial advertisement calls of the male cricket Teleogryllus commodus and played them back to females in laboratory phonotaxis trials to estimate the linear and nonlinear sexual selection that female phonotactic choice imposes on male call structure. Significant nonlinear selection on the major axes of the fitness surface was convex in nature and displayed an intermediate optimum, indicating multivariate stabilizing selection. The mean phenotypes of four independent samples of males, from the same population as the females used in phonotaxis trials, were within the 95% confidence region for the fitness peak. These experiments indicate that stabilizing sexual selection may play an important role in the evolution of male call properties in natural populations of T. commodus.     

Signatures of contemporary selection in the Israeli Holstein dairy cattle

Strong selection in the Israeli Holstein dairy cattle population over the last three decades should have left clear signatures of selection. Two experimental approaches were applied to detect evidence of contemporary selection based on the 54K BeadChip genotypes of ~1000 Israeli Holstein bulls: (i) the long-range haplotype test, which searches for structural evidence resulting from selective sweep, and (ii) direct analysis of the changes in haplotypes frequencies over time combined with linkage disequilibrium blocks haplotype-based association analysis. Ten traits were analyzed: the PD07 Israeli selection index, milk, milk fat, % fat, milk protein, % protein, somatic cell score, female fertility, milk production persistency and herd life. The long-range haplotype test detected ~15% of the 3288 haplotypes that showed significant positive frequency trends (P < 0.05) and was significantly correlated with the substitution effects of the haplotypes and the selection intensities for the different traits. Thirty signatures of recent selection, which correspond to both approaches and affect the Israeli PD07 selection index, were identified on 17 of the 29 autosomes. The second experimental approach also was used to estimate the selection intensity of the different traits. The correlation between the selection intensities for the traits analyzed, derived from changes in haplotype frequencies in the population of bulls, and those derived from trait-based analysis of the cow population was 0.93 over all traits. Thus, the changes in haplotypes frequencies in the bulls' population accurately estimate genetic trends in the general cow population and can be used to detect signatures of recent selection.     

大豆航天搭载SP4选择效果与SP2代变异率相关分析

摘要：为了明确大豆航天搭载早期世代农艺性状选择的依据,提高航天搭载育种早期世代选择效果。对6个大豆品种经过航天搭载后的SP2代变异率和SP4代选择效果进行了分析,结果表明遗传力高的SP2代的单株荚数和单株粒数2个农艺性状的变异率与SP4代入选单株数相关达到极显著水平;SP2代遗传力较高底荚高度和节间长度的变异率与SP4代入选单株相关达到显著水平,SP2代遗传力不高的植株高度和主茎节数变异率与SP4代入选单株相关不显著;SP2代对单株荚数、单株粒数、底荚高度、节间长度进行选择有效,而对植株高度和主茎节数选择效果不明显。     

Opportunities of marker-assisted selection for Plum pox virus resistance in apricot breeding programs

Evaluation of Plum pox virus (PPV) resistance is a laborious and expensive task, and the development of new accurate methods, including the use of molecular markers, would be very useful for breeding programs for resistance. In this work, the Plum pox virus resistance of 80 apricot genotypes of different genetic origins was evaluated in controlled greenhouse and natural field conditions. The genotypes for five simple sequence repeat (SSR) markers described as linked to PPV resistance were also determined. Depending on their behavior, cultivars were classified as resistant, susceptible, and uncertain, and the genotype was identified for each SSR linked to different phenotypes. Twenty genotypes were resistant and 37 susceptible in the greenhouse and in the field. However, 23 genotypes did not show clear behavior, probably due to the complex plant-virus interaction, so they were classified as uncertain. In general, results showed a narrow relationship between the SSRs PGS1.21 and PGS1.24, and resistance to PPV, although some genotypes did not show this relationship. Most of the susceptible genotypes did not show the alleles of resistance. Therefore, in most cases, marker-assisted selection (MAS) could be used as a means of screening new seedlings for early selection, making it possible to remove those that are susceptible. However, in certain cases, MAS using these markers has not proven to be completely effective. The origin of such discrepancies could be the presence of a second locus involved in PPV resistance. In addition, other factors affecting efficiency of MAS discussed in the work are the presence of null alleles and recombinant events. Resistant seedlings would have to be evaluated in greenhouse and natural conditions to confirm their actual behavior against PPV. From the breeding point of view, the use of homozygous resistant parents for the SSR resistance alleles, with good agronomic characteristics, would increase the efficiency of breeding programs, since all seedlings would be resistant regardless of the other parent. Finally, new molecular markers should be developed to accurately select resistant seedlings regardless of the resistant progenitors involved.     

Genomic Prediction of Testcross Performance in Canola (Brassica napus)

Genomic selection (GS) is a modern breeding approach where genome-wide single-nucleotide polymorphism (SNP) marker profiles are simultaneously used to estimate performance of untested genotypes. In this study, the potential of genomic selection methods to predict testcross performance for hybrid canola breeding was applied for various agronomic traits based on genome-wide marker profiles. A total of 475 genetically diverse spring-type canola pollinator lines were genotyped at 24,403 single-copy, genome-wide SNP loci. In parallel, the 950 F1 testcross combinations between the pollinators and two representative testers were evaluated for a number of important agronomic traits including seedling emergence, days to flowering, lodging, oil yield and seed yield along with essential seed quality characters including seed oil content and seed glucosinolate content. A ridge-regression best linear unbiased prediction (RR-BLUP) model was applied in combination with 500 cross-validations for each trait to predict testcross performance, both across the whole population as well as within individual subpopulations or clusters, based solely on SNP profiles. Subpopulations were determined using multidimensional scaling and K-means clustering. Genomic prediction accuracy across the whole population was highest for seed oil content (0.81) followed by oil yield (0.75) and lowest for seedling emergence (0.29). For seed yieId, seed glucosinolate, lodging resistance and days to onset of flowering (DTF), prediction accuracies were 0.45, 0.61, 0.39 and 0.56, respectively. Prediction accuracies could be increased for some traits by treating subpopulations separately; a strategy which only led to moderate improvements for some traits with low heritability, like seedling emergence. No useful or consistent increase in accuracy was obtained by inclusion of a population substructure covariate in the model. Testcross performance prediction using genome-wide SNP markers shows considerable potential for pre-selection of promising hybrid combinations prior to resource-intensive field testing over multiple locations and years.     

Transmission of important chromosomal regions under selection revealed in rice pedigree breeding programs

Genetic analysis across a whole plant genome based on pedigree information offers considerable potential for enhancing genetic gain from plant breeding programs through quantitative trait loci (QTL) mapping and marker-assisted selection. Here, we report its application for graphically genotyping varieties used in Chinese japonica rice (Oryza sativa L.) pedigree breeding programs. We identified 34 important chromosomal regions from the founder parent that are under selection in the breeding programs, and by comparing donor genomic regions that are under selection with QTL locations of agronomic traits, we found that QTL clustered in important genomic regions, in accordance with association analyses of natural populations and other previous studies. The convergence of genomic regions under selection with QTL locations suggests that donor genomic regions harboring key genes/QTL for important agronomic traits have been selected by plant breeders since the 1950s from the founder rice plants. The results provide better understanding of the effects of selection in breeding programs on the traits of rice cultivars. They also provide potentially valuable information for enhancing rice breeding programs through screening candidate parents for targeted molecular markers, improving crop yield potential and identifying suitable genetic material for use in future breeding programs.     

Evaluation of tomato genotypes for resistance to whitefly (Bemisia tabaci Gennadius) and tomato leaf curl virus in eastern India

Tomato production in the tropics is threatened by whitefly infestation and tomato leaf curl virus (ToLCV) causing severe economic losses. No stable resistance to these biotic challenges has been identified in eastern India. Therefore, initial screening of 19 advance breeding lines of tomato was carried out during the year 2016–17. Based on the whitefly population per leaf and tomato leaf curl disease severity, eight tomato genotypes were selected for final screening during the year 2017–18. Morphological leaf traits and biochemical parameters in tomato leaf were assessed in selected genotypes and considered as potential mediators of resistance. Significant variation was observed for whitefly infestation and ToLCV disease severity among the tomato genotypes tested. Higher leaf trichome density with narrow and thinner leaves and higher total phenol content in leaf emerged as reliable morphological and biochemical markers for early selection of tomato genotype resistant to whitefly and ToLCV disease. The resistance of tomato genotypes 2016/Res-1, 2015/Res-5, 2014/Res-1 and 2014/Res-4 to both whitefly and ToLCV disease is based on antixenotic properties and they could be utilized in future breeding to enhance stable resistance against these biotic challenges.