Pleiotropic Effect Analysis and Marker Development for Grain Zinc and Iron Concentrations in Spring wheat

Wheat (Triticum aestivum L.) is one of the main food crops in the world and a primary source of zinc (Zn) and iron (Fe) in the human body. The genetic mechanisms underlying related traits have been clarified, thereby providing a molecular theoretical foundation for the development of germplasm resources. In this study, 23,536 high-quality DArT markers were used to map quantitative trait loci (QTL) of grain Zn (GZn) and grain Fe (GFe) concentrations in recombinant inbred lines from Avocet/Chilero. A total of 17 QTLs located on chromosomes 1BL, 2BL, 3BL, 4AL, 4BS, 5AL, 5DL, 6AS, 6BS, 6DS, and 7AS accounted for 0.38–16.62% of the phenotypic variance. QGZn.haust-4AL, QGZn.haust-7AS.1, and QGFe.haust-6BS were detected on chromosomes 4AL, 6BS, and 7AS, accounting for 10.63–16.62% of the phenotypic variance. Four stable QTLs, QGZn.haust-4AL, QGFe.haust-1BL, QGFe.haust-4AL, and QGFe.haust-5DL were located on chromosomes 1BL, 4AL, and 5DL. Three pleiotropic effects locus for GZn and GFe concentrations were located on chromosomes 1BL, 4AL, and 5DL. Two high-throughput Kompetitive Allele Specific PCR markers were developed by closely linking single nucleotide polymorphisms on chromosomes 4AL and 5DL, which were validated by a germplasm panel. Therefore, it is the most important that quantitative trait loci and KASP marker for grain zinc and iron concentrations were developed for utilizing in marker-assisted breeding and biofortification of wheat grain in breeding programs.

Localization of QTL for cold tolerance at the germination stage of rice (Oryza sativa L.) using recombinant inbred lines

The cold tolerance of germinating direct-sown rice (Oryza sativa L.) has an increased rate of emergence, which ensures vigorous seedling growth. Research on QTL localization for cold tolerance at the germination stage can assist in molecular marker-assisted selection and enhance breeding efficiency. In this study, 94 populations of recombinant self-incompatible lines from Heigu and Ha 9366 were selected to investigate germination rates at low temperatures. It was found that two QTL loci (qLTG-3 and qLTG-12) were located at different germination times on chromosomes 3 and 12, respectively. The two QTLs at three different germination times, located using QTL, accounted for 21.3–25.9% of the phenotypic variation. Moreover, a reciprocal effect was detected between the two QTLs. The double QTLs increased the germination rate by 22–27% in this population. Additionally, qLTG-12 improved cold tolerance at the seedling stage. The results of this study might provide the materials and molecular markers for future molecular marker-assisted breeding for cold tolerance at the germination stage.

Recombinant inbred lines and next-generation sequencing enable rapid identification of candidate genes involved in morphological and agronomic traits in foxtail millet

We constructed recombinant inbred lines (RILs) between a Japanese and a Taiwanese landrace of foxtail millet and employed next-generation sequencing, such as flexible ddRAD-seq and Nanopore sequencing to identify the candidate genes involved in the crop evolution of foxtail millet. We successfully constructed a linkage map using flexible ddRAD-seq with parents and RILs and detected major QTLs for each of three traits: leaf sheath colors, spikelet-tipped bristles (stb), and days to heading (DTH). (1) For leaf sheath colors, we identified the C gene on chromosome IV. (2) We identified a homeobox (HOX14) gene for stb on chromosome II, which shows homology with HvVrs1 in barley. (3) Finally, we identified a QTL with a large effect on DTH on chromosome II. A parent of the RILs from Taiwan and Yugu1 had a Harbinger-like TE in intron 3 of this gene. We also investigated the geographical distribution of the TE insertion type of this gene and found that the insertion type is distributed in the northern part of East Asia and intensively in South and Southeast Asia, suggesting that loss/reduction of function of this gene plays an important role in spreading into the northern part of East Asia and subtropical and tropical zones.

Powerful, efficient QTL mapping in Drosophila melanogaster using bulked phenotyping and pooled sequencing

Despite the value of Recombinant Inbred Lines (RILs) for the dissection of complex traits, large panels can be difficult to maintain, distribute, and phenotype. An attractive alternative to RILs for many traits leverages selecting phenotypically extreme individuals from a segregating population, and subjecting pools of selected and control individuals to sequencing. Under a bulked or extreme segregant analysis paradigm, genomic regions contributing to trait variation are revealed as frequency differences between pools. Here we describe such an extreme quantitative trait locus, or X-QTL, mapping strategy that builds on an existing multiparental population, the DSPR (Drosophila Synthetic Population Resource), and involves phenotyping and genotyping a population derived by mixing hundreds of DSPR RILs. Simulations demonstrate that challenging, yet experimentally tractable X-QTL designs ( > =4 replicates, > =5000 individuals/replicate, and selecting the 5-10% most extreme animals) yield at least the same power as traditional RIL-based QTL mapping and can localize variants with sub-centimorgan resolution. We empirically demonstrate the effectiveness of the approach using a 4-fold replicated X-QTL experiment that identifies 7 QTL for caffeine resistance. Two mapped X-QTL factors replicate loci previously identified in RILs, 6/7 are associated with excellent candidate genes, and RNAi knock-downs support the involvement of 4 genes in the genetic control of trait variation. For many traits of interest to drosophilists, a bulked phenotyping/genotyping X-QTL design has considerable advantages.

Relationship between the Characteristics of Bread Wheat Grains, Storage Time and Germination

Seed storage is important to farmers, breeders and for germplasm preservation. During storage, seeds accumulate damage at the structural and metabolic level, which disrupt their function and reduce resistance to adverse external conditions. In this regard, issues related to seed aging prove to be relevant for maintaining the viability of genetic collections. We analyzed morphological characteristics of grains and their coat color for 44 recombinant inbred lines (RILs) of bread wheat grown in four different seasons, 2003, 2004, 2009 and 2014. Our investigations were performed in 2020. For 19 RILs from the same seasons germination was evaluated. Our results demonstrate that genotype significantly affects the variability of all seed traits, and the year of harvesting affects about 80% of them (including all the traits of shape and size). To identify the trend between changes in grain characteristics and harvesting year, we estimated correlation coefficients between them. No significant trend was detected for the grain shape/size traits, while 90% of the color traits demonstrated such a trend. The most significant negative correlations were found between the harvesting year and the traits of grain redness: the greater the storage time, the more intensive is red color component for the grains. At the same time, it was shown that grains of longer storage time (earlier harvesting year) have lighter coat. Analysis of linear correlations between germination of wheat seeds of different genotypes and harvesting years and their seed traits revealed a negative linear relationship between the red component of coat color and germination: the redder the grains, the lower their germination rate. The results obtained demonstrate manifestations of metabolic changes in the coat of grains associated with storage time and their relationship with a decrease of seed viability.

Validation of Genomic Selection Approach for Predicting Sheath Blight Resistance in Rice (Oryza sativa L.,)

Rice sheath blight (ShB) is one of the most serious fungal diseases caused by Rhizoctonia solani, instigating significant yield losses in many rice-growing regions of the world. Intensive studies indicated that resistance for sheath blight is controlled possibly by polygenes. Because of complex inheritance, it’s very difficult to exploit and tap all the genomic regions conferring resistance using classical approaches of QTL mapping, it’s very important to have a different strategy to harness such resistance mechanism. One promising approach that can potentially provide accurate predictions of the resistance phenotypes is genomic selection (GS). The research was undertaken with an objective to validate genomic selection approach for predicting sheath blight resistance involving 1545 Recombinant inbred lines (RILs) derived from eleven crosses between resistant and susceptible parents (Jasmine 85XTN1, Jasmine 85XSwarnaSub1, Jasmine 85XII32B, Jasmine 85XIR54, TetepXTN1, TetepXSwarna Sub1, TetepXII32B, TetepXIR54, MTU 9992XTN1, MTU 9992XII32B and MTU 9992XIRBB4). Where, Jasmine 85, Tetep & MTU 9992 were resistant parents and TN1, Swarna Sub1, II32B, IR54 & IRBB4 were susceptible parents. During rainy season (2020) the F7 RILs were screened for their reaction to sheath blight in two hot spot locations. The genotyping was done with Illumina platform having 6564 SNP markers. Bayesian B approach was used to train the statistical model for calculation of marker effects and GEBVs. The prediction accuracy of training set (data fit analysis) obtained was 0.70 and random cross validation with different approaches, the prediction accuracy ranged from 0.67 to 0.74. The results are lucrative, all in all, high prediction accuracies observed in this study suggest genomic selection as a very promising breeding strategy for predicting sheath blight resistance in Rice.

Cross-Kingdom Gene Coexpression Analysis Using a Stemphylium botryosum–Lens ervoides System Revealed Plasticity of Intercommunication Between the Pathogen Secretome and the Host Immune Systems

Necrotrophic pathogens are responsible for significant declines in crop yield and quality worldwide. During the infection process, a pathogen releases a series of secretory proteins to counteract the plant immune system, and this interaction of pathogen and host molecules determines whether the pathogen will successfully invade the host plant tissues. In this study, we adopted co-transcriptomic approaches to analyze the Lens ervoides–Stemphylium botryosum system, with a focus on 1,216 fungal genes coding for secretory proteins and 8,810 disease-responsive genes of the host 48, 96, and 144 h postinoculation, captured in two F9 recombinant inbred lines (RILs) displaying contrasting disease responses. By constructing in planta gene coexpression networks (GCNs) for S. botryosum, we found that the pathogen tended to co-upregulate genes regulating cell wall degradation enzymes, effectors, oxidoreductases, and peptidases to a much higher degree in the susceptible host LR-66-577 than in the resistant RIL LR-66-637, indicating that the promotion of these digestive enzymes and toxins increased S. botryosum virulence. Construction of cross-kingdom GCNs between pathogen and plant for the two RILs revealed that the co-upregulation of these fungal digestive enzymes and toxins simultaneously promoted a series of defense responses such as redox change, expression of membrane-related genes and serine/threonine kinase, and stress and disease responses in the susceptible RIL which was not observed in the resistant RIL, indicating that these activities exacerbated susceptibility to S. botryosum. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Novel QTL and Meta-QTL Mapping for Major Quality Traits in Soybean

Isoflavone, protein, and oil are the most important quality traits in soybean. Since these phenotypes are typically quantitative traits, quantitative trait locus (QTL) mapping has been an efficient way to clarify their complex and unclear genetic background. However, the low-density genetic map and the absence of QTL integration limited the accurate and efficient QTL mapping in previous researches. This paper adopted a recombinant inbred lines (RIL) population derived from ‘Zhongdou27’and ‘Hefeng25’ and a high-density linkage map based on whole-genome resequencing to map novel QTL and used meta-analysis methods to integrate the stable and consentaneous QTL. The candidate genes were obtained from gene functional annotation and expression analysis based on the public database. A total of 41 QTL with a high logarithm of odd (LOD) scores were identified through composite interval mapping (CIM), including 38 novel QTL and 2 Stable QTL. A total of 660 candidate genes were predicted according to the results of the gene annotation and public transcriptome data. A total of 212 meta-QTL containing 122 stable and consentaneous QTL were mapped based on 1,034 QTL collected from previous studies. For the first time, 70 meta-QTL associated with isoflavones were mapped in this study. Meanwhile, 69 and 73 meta-QTL, respectively, related to oil and protein were obtained as well. The results promote the understanding of the biosynthesis and regulation of isoflavones, protein, and oil at molecular levels, and facilitate the construction of molecular modular for great quality traits in soybean.

​Character Association and Path Analysis in Heterotic Recombinant Inbred Lines in Garden Pea (Pisum sativum L.)

Background: Garden pea is one of the principal vegetable crops cultivated in the temperate and sub- tropical areas of the world for its green pods. It is an important food legume worldwide after Phaseolus vulgaris. The knowledge about the interdependence of characters in a particular crop can effectively be employed to breed desirable cultivars and to challenge the consequences of the unprecedented biological, physical and chemical stresses of the future growing conditions. The regression and path analysis further has significance for the assured selection of the varieties with desirable traits and hence adaptation of species in different agro-climatic conditions; hence it is also one of the prerequisites for crop improvement programmes. Correlation and path analysis in garden pea explained that among all the yield contributing traits, number of pods per plant and pod weight have significant contribution in increasing the green pod yield per plant. Methods: 14 heterotic recombinant inbred lines and 17 existing cultivars of garden pea, were put to experimentation for working out the association of the yield and yield contributing component characters under the open field conditions of Regional Horticultural Research and Training Station, Bajaura Kullu, Himachal Pradesh, India. This association was further elaborated through the coefficient of correlation and regression analysis and path coefficient analysis. Result: The genotypic correlation coefficients were found higher than the phenotypic correlation coefficients for all the characters studied. The correlation coefficients revealed that green pod yield per plant had highly significant and positive association with pod weight and number of pods per plant. The path coefficient analysis also revealed that the maximum positive direct effect on green pod yield per plant was exerted by the number of pods per plant, pod weight and 100-seed weight. Through regression equation analysis it became clear that number of pods per plant, pod weight contributed significantly in increasing the green pod yield per plant. With a unit increase in these independent characters, the green pod yield per plant will increase by 2.34 and 33.45 per cent. It can thus be concluded that despite of the positive correlation of almost all the characters with green pod yield per plant, only number of pods per plant and pod weight are important and significant independent characters for increasing the green pod yield per plant.

Genetic, Epigenetic, Genomic and Microbial Approaches to Enhance Salt Tolerance of Plants: A Comprehensive Review

Globally, soil salinity has been on the rise owing to various factors that are both human and environmental. The abiotic stress caused by soil salinity has become one of the most damaging abiotic stresses faced by crop plants, resulting in significant yield losses. Salt stress induces physiological and morphological modifications in plants as a result of significant changes in gene expression patterns and signal transduction cascades. In this comprehensive review, with a major focus on recent advances in the field of plant molecular biology, we discuss several approaches to enhance salinity tolerance in plants comprising various classical and advanced genetic and genetic engineering approaches, genomics and genome editing technologies, and plant growth-promoting rhizobacteria (PGPR)-based approaches. Furthermore, based on recent advances in the field of epigenetics, we propose novel approaches to create and exploit heritable genome-wide epigenetic variation in crop plants to enhance salinity tolerance. Specifically, we describe the concepts and the underlying principles of epigenetic recombinant inbred lines (epiRILs) and other epigenetic variants and methods to generate them. The proposed epigenetic approaches also have the potential to create additional genetic variation by modulating meiotic crossover frequency.