Plant Breeding Methods Research Articles

Registration of R.LBK1 and R.LBK2 Sorghum Germplasm with Resistance to the Sugarcane Aphid [Melanaphis sacchari (Zehntner)

The sorghum [Sorghum bicolor (L.) Moench] germplasm lines R.LBK1 (Reg. No. GP‐865, PI 687244) and R.LBK2 (Reg. No. GP‐866, PI 687245) were developed and released by the USDA in Lubbock, TX, in 2017 because of their high degree of resistance to the sugarcane aphid (SCA) [Melanaphis sachari (Zehntner) (Hempitera: Aphidae)]. Both lines were developed using the pedigree method of plant breeding and are confirmed to be restorer lines. The breeding crosses for both lines were made in Lubbock, TX, and selections were made in Lubbock and Corpus Christi, TX. Evaluation for SCA resistance was conducted in two field locations in Texas in 2016, as well as a greenhouse experiment at the USDA‐ARS laboratory in Lubbock. Both lines express strong resistance to SCA pressures at both seedling and mature plant stages. Preliminary hybrids using highly susceptible seed parents have also shown strong resistance to SCA, indicating that the resistance is dominantly expressed in F1 hybrids using these two lines. R.LBK1 and R.LBK2 are not completely immune to the SCA, but damage is greatly reduced and resistance is extremely apparent when compared to other susceptible sorghum lines and hybrids. These lines provide much needed resistance to the SCA and are suitable as germplasm in a plant breeding program or as parental lines for hybrid development.

SOME ASPECTS OF BREEDING OF MEDICINAL AND AROMATIC PLANTS

Plants have been exploited a source of medicines throughout human history and in all cultures. Scientific progress has allowed us to identify a minor fraction of the active compounds and their modes of action. Subsequently, it has greatly contributed to the development of modern medicines. Though, there is no suspicion that the biological information of how to synthesize the extremely complex bio-active compounds is involved within genome of medicinal plants. In the genomic era, medicinal plants are not represented only a source of chemical constituents, possessing acquired a new interest, but also serve as a source of genes included in formation of active principles. Thus, it represents as joint duty not only to derive information from these plants and to exploit this information wisely, but also to preserve them for future generations. Therefore, hence some highlights are provided on some thoughts that dealt with traditional methods of plant breeding applied on medicinal and aromatic plants thereby other thoughts are extracted supplemented with references to elucidate the multifaceted aspects for medicinal purposes.furthermore, it was referred to some early selection methods using recent statistical techniques as GGE Biplot, AMMI Biplot and ternary plot.

Poplar miR472a targeting NBS-LRRs is involved in effective defence against the necrotrophic fungus Cytospora chrysosperma.

The hemibiotroph Colletotrichum gloeosporioides and the necrotroph Cytospora chrysosperma cause poplar foliage and stem disease, respectively, resulting in substantial economic losses. In this study, Populus trichocarpa ptc-miR472a was down-regulated in leaves treated with salicylic acid, jasmonic acid (JA) or bacterial flagellin (flg22). Here, ptc-miR472a and a short tandem target mimic (STTM) of miR472a were overexpressed in P. alba × P. glandulosa, and overexpression lines of miR472a and silenced lines of STTM472a were generated. Compared with the STTM472a and wild type lines, lower reactive oxygen species accumulation was detected in miR472a overexpressing plants treated with flg22, C. gloeosporioides or C. chrysosperma. In addition, the miR472a overexpressing lines exhibited the highest susceptibility to the hemibiotroph, C. gloeosporioides, but the highest effective defence response to the necrotroph, C. chrysosperma. The JA/ethylene marker gene ERF1 was rapidly up-regulated in miR472a overexpressing plants. Furthermore, five phased, secondary, small interfering RNAs (phasiRNAs) were confirmed in the miR472a overexpressing and STTM472a lines, triggering phasiRNAs predicted to enhance NBS-LRR silencing. Taken together, our results revealed that ptc-miR472a exerts a key role in plant immunity to C. gloeosporioides and C. chrysosperma by targeting NBS-LRR transcripts. This study provides a new strategy and method in plant breeding to improve plant disease resistance.

Registration of RTx3410 through RTx3428 Sorghum Germplasm Resistant to Sugarcane Aphid [Melanaphis sacchari (Zehntner)

The sorghum [Sorghum bicolor (L.) Moench] germplasm lines RTx3410 through RTx3428 (Reg. No. GP‐846 to GP‐864, PI 686993 to PI 687011) were developed and released by Texas A&M AgriLife Research, Lubbock, TX, in 2018. The lines are resistant to damage caused by the sugarcane aphid [Melanaphis sacchari (Zehntner) (Hemiptera: Aphididae)] (SCA). All lines were developed by intentional plastic bag emasculation crosses and selected using the pedigree method of plant breeding. Resistance in RTx3410 through RTx3426 was identified after the SCA became a consistent pest of sorghum in the United States in 2013. To develop RTx3427 and RTx3428, crosses and selections were made in the Texas A&M AgriLife Research program at various Texas locations and resistance to the SCA in southern Africa was identified in Botswana and South Africa. Resistance in the United States was confirmed following identification of virulent SCA in 2013. All lines at seedling and adult plant stages expressed moderate to high levels of resistance to SCA. Resistance in RTx3412 to RTx3426 is derived either from Tx2783 or an early generation sib. Resistance in RTx3410, RTx3411, RTx3427, and RTx3248 is from unknown sources of resistance. The genetic relationship between the resistance gene(s) from the different sources is not known. The lines with potentially diverse sources of resistance provide the sorghum industry with a diversity of elite germplasm with resistance to SCA.

Genomic Prediction Using Prior Quantitative Trait Loci Information Reveals a Large Reservoir of Underutilised Blackleg Resistance in Diverse Canola (Brassica napus L.) Lines.

Genomic prediction is becoming a popular plant breeding method to predict the genetic merit of lines. While some genomic prediction results have been reported in canola, none have been evaluated for blackleg disease. Here, we report genomic prediction for seedling emergence, survival rate, and internal infection), using 532 Spring and Winter canola lines. These lines were phenotyped in two replicated blackleg disease nurseries grown at Wickliffe and Green Lake, Victoria, Australia. A transcriptome genotyping-by-sequencing approach revealed 98,054 single nucleotide polymorphisms (SNPs) after quality control. We assessed various genomic prediction scenarios based on Genomic Best Linear Unbiased Prediction (GBLUP), BayesR and BayesRC, which can make use of prior quantitative trait loci information, via cross-validation. Clustering based on genomic relationships showed that Winter and Spring lines were genetically distinct, indicating limited gene flow between sets. Genetic correlations within traits between Spring and Winter lines ranged from 0.68 and 0.90 (mean = 0.76). Based on GBLUP in the whole population, moderate to high genomic prediction accuracies were achieved within environments (0.35-0.74) and were reduced across environments (0.28-0.58). Prediction accuracy within the Spring set ranged from 0.30-0.69, and from 0.19-0.71 within the Winter set. The BayesR model resulted in slightly lower accuracy to GBLUP. The proportion of genetic variance explained by known blackleg quantitative trait loci (QTL) was < 30%, indicating that there is a large reservoir of genetic variation in blackleg traits that remains to be discovered, but can be captured with genomic prediction. However, providing prior information of known QTL in the BayesRC method resulted in an increased prediction accuracy for survival and internal infection, particularly with Spring lines. Overall, these promising results indicate that genomic prediction will be a valuable tool to make use of all genetic variation to improve blackleg resistance in canola.

In vitro propagation of Digitalis lanata Ehrh. through direct shoot regeneration – A source of cardiotonic glycosides

An efficient method for the in vitro propagation of Digitalis lanata Ehrh. through direct organogenesis from leaf and petiole explants has been standardised. MS basal medium supplemented with cytokinins BAP, KIN, TDZ either alone or along with auxins IAA and NAA at different concentrations were tried. TDZ at 4.54 and 6.81 μmol/l were optimum for direct regeneration of shoots from leaf (4.4 ± 0.6 shoots/explant), and petiole (3.0 ± 0.8 shoots/explant) explants respectively. Among the various concentrations of auxins IAA, IBA and NAA tried for rooting, the best response occurred on MS basal medium supplemented with 17.13 μmol/l IAA. On greenhouse transfer about 60% of the plantlets survived. In vitro raised plantlets were morphologically similar to mother plants. Cardiotonic glycosides digoxin and digitoxin were extracted by modified methods and estimated by HPLC. There were no significant differences in digoxin and digitoxin content in leaves of naturally grown and in vitro raised plants. The method for in vitro propagation of D. lanata through direct organogenesis from leaf and petiole explants reported here will be of great use for the rapid and large scale clonal propagation, production of biomass for extraction of cardiotonic glycosides, ex situ conservation, and improvement through conventional plant breeding and transgenic methods.

The Nobel Laureates’ Campaign Supporting GMOs

More than 800 million people suffer from hunger in the world. Using modern plant breeding methods to generate so-called GMOs (Genetically Modified Organisms), agricultural scientists have shown that crop yields and nutritional quality can be greatly improved. Many GMO varieties have been specifically developed with the aim of being resistant to pests, tolerant to drought and containing beneficial nutrients. This leads to a reduction in the use of insecticides in water and on land. If anything, the GMO varieties are safer than traditionally bred varieties because they are made in a very precise manner. However, the scientific evidence on this issue is being ignored by the Green Parties such as Greenpeace who continue to deny the science and mislead the public. 129 Nobel Laureates have joined in a campaign to convince the Green Parties and the public that they should support the use of GMOs, especially for the sake of the developing world.

Do consumers care how a genetically engineered food was created or who created it?

This paper explores heterogeneity in consumer preferences for foods and policies that relate to different innovative plant breeding technologies. As a starting point in our analysis, we report results from almost four years of monthly surveys with U.S. consumers, which show slight food safety concern for genetically engineered food with no discernable trend of increased or decreased concern over time. We find small differences in consumer preferences for policies related to different plant breeding methods, with the strongest support for the notion that bioengineered crops should be regulated based on health and environmental outcomes rather than the process used to create new crops. Other survey results reveal support or opposition for genetically engineered food depends on consumers’ perceptions of who created the technology. We also find that food safety concerns related to genetically engineered food are related to perceptions about the distribution of benefits from the technology across the food supply chain.

Assessment of RAPD Markers to Analyse the Genetic Diversity among Sunflower (Helianthus annuus L.) Genotypes

Genetic diversity estimation among different species is an important tool for genetic improvement to maximize the yield, desirable quality, wider adaptation, pest and insect resistance that ultimately boosting traditional plant breeding methods. The most efficient way of diversity estimation is application of molecular markers. In this study, twenty random amplified polymorphic DNA (RAPD) primers were utilized to estimate the genetic diversity between ten sunflower genotypes. Overall 227 bands were amplified by 20 primers with an average of 11.35 bands per primer. RAPD data showed 86.34% polymorophic bands and 13.65% of monomorophic bands. Genetic similarity was ranged from 50.22% to 87.22%. The lowest similarity (50.22%) was observed between FH-352 and FH-359 and the maximum similarity 87.22% was observed between A-23 and G-46. Polymorphic information content (PIC) values were varying from 0.05 to 0.12 with a mean of 0.09. Cluster analysis based on RAPD results displayed two major distinct groups 1 and 2. Group-2 contains FH-352 which was the most diverse genotype, while group-1 consists of few sub groups with all other genotypes. Ample diversity was found in all the genotypes. Present study reveals novel information about sunflower genome which can be used in future studies for sunflower improvement.

Efficient genome-wide genotyping strategies and data integration in crop plants.

Next-generation sequencing (NGS) has revolutionized plant and animal research by providing powerful genotyping methods. This review describes and discusses the advantages, challenges and, most importantly, solutions to facilitate data processing, the handling of missing data, and cross-platform data integration. Next-generation sequencing technologies provide powerful and flexible genotyping methods to plant breeders and researchers. These methods offer a wide range of applications from genome-wide analysis to routine screening with a high level of accuracy and reproducibility. Furthermore, they provide a straightforward workflow to identify, validate, and screen genetic variants in a short time with a low cost. NGS-based genotyping methods include whole-genome re-sequencing, SNP arrays, and reduced representation sequencing, which are widely applied in crops. The main challenges facing breeders and geneticists today is how to choose an appropriate genotyping method and how to integrate genotyping data sets obtained from various sources. Here, we review and discuss the advantages and challenges of several NGS methods for genome-wide genetic marker development and genotyping in crop plants. We also discuss how imputation methods can be used to both fill in missing data in genotypic data sets and to integrate data sets obtained using different genotyping tools. It is our hope that this synthetic view of genotyping methods will help geneticists and breeders to integrate these NGS-based methods in crop plant breeding and research.

Ekonomika proizvodnje paradajza u zavisnosti od načina nabavke rasada

The aim of the paper is to calculate and compare the economic indicators in the production of tomatoes in protected areas for two methods of plant breeding: production of seedlings on the agricultural holding and when seedlings are purchased on the market. The results show that the production of tomatoes with farmers' own seedlings is economically more profitable than the method which implies the purchase of seedlings. After calculating the relative indicators of success of production, it was found that the production of tomatoes was economically viable in both ways, but significantly more profitable when seedlings were produced on a farmer's own farm. The obtained profitability coefficient of 2.576 indicates that 2.576 dinars of revenues are achieved for every 1 dinar of expenses. If tomato seedlings were purchased, the profitability coefficient would be 2.078, but production would still be economically viable. The profitability of production coefficient indicates that for every 100 dinars invested, we can make a net profit of 157.6 dinars when seedlings are home-grown, or we can make a net profit of 107.81 dinars when the seedlings are purchased on the market.

Yield Evaluation and Interrelationship between Yield Related Traits in Advance Lines of Mustard through Correlation Studies

Purpose: Pakistan is spending a large amount of foreign exchange on the import of edible oil every year. The present experiment was conducted to study the relationship between different seed yield related traits in advance lines of Brassica juncea developed through pedigree method of plant breeding. The seed yield performance of these advance lines was also evaluated during the experiment. Research Method: Twelve lines were grown in Randomized Complete Block Design with three replications during September 2016. All recommended cultural practices were used throughout the experiment. The data for plant height, days to flowering, days to maturity, branches per plant, seeds per silique, seed yield per plot and oil% was collected. Findings: The correlation analysis revealed that seed yield per plot was highly and significantly correlated with the number of branches per plant and seeds per siliqua. ZBJ-13006 & ZBJ-15009 produced significantly higher seed yield (2.21kg/plot) & (2.10kg/plot) respectively than the check variety AARI Canola. Research limitations: Although the study was carefully carried out and reached its aim, environmental conditions were unavoidable limitations. Originality/Value: The present study has clearly indicated the need for giving due weightage for the number of seeds per siliqua and the number of branches per plant for improving seed yield in Mustard.

In vitro regeneration of some economically important elite Indica rice genotypes

Rice is an inherent part of human civilization and consumed by majority of Asians as their staple food. In addition to classical plant breeding methods, biotechnological tools including genetic engineering and genome editing are important for rice improvement to meet the growing demand. Both genetic engineering and genome editing technology are dependent on in vitro tissue culture and regeneration. Indica rice genotypes are widely known as recalcitrant in in vitro culture system. In the present study, we evaluated tissue culture responsiveness of 20 Indica rice genotypes known for important characters and standardized the suitable hormone combination for regeneration of each of those genotypes. Regenerated plantlets were successfully rooted and were acclimated to ex vitro condition. ISSR fingerprinting revealed monomorphic banding pattern between regenerated and control plants indicating the suitability of those regeneration media to maintain genetic fidelity. Results of the present study could be used efficiently in genetic transformation studies of Indica rice, which in turn would accelerate rice crop improvement.

Parent-progeny imputation from pooled samples for cost-efficient genotyping in plant breeding.

The increased usage of whole-genome selection (WGS) and other molecular evaluation methods in plant breeding relies on the ability to genotype a very large number of untested individuals in each breeding cycle. Many plant breeding programs evaluate large biparental populations of homozygous individuals derived from homozygous parent inbred lines. This structure lends itself to parent-progeny imputation, which transfers the genotype scores of the parents to progeny individuals that are genotyped for a much smaller number of loci. Here we introduce a parent-progeny imputation method that infers individual genotypes from non-barcoded pooled samples of DNA of multiple individuals using a Hidden Markov Model (HMM). We demonstrate the method for pools of simulated maize double haploids (DH) from biparental populations, genotyped using a genotyping by sequencing (GBS) approach for 3,000 loci at 0.125x to 4x coverage. We observed high concordance between true and imputed marker scores and the HMM produced well-calibrated genotype probabilities that correctly reflected the uncertainty of the imputed scores. Genomic estimated breeding values (GEBV) calculated from the imputed scores closely matched GEBV calculated from the true marker scores. The within-population correlation between these sets of GEBV approached 0.95 at 1x and 4x coverage when pooling two or four individuals, respectively. Our approach can reduce the genotyping cost per individual by a factor up to the number of pooled individuals in GBS applications without the need for extra sequencing coverage, thereby enabling cost-effective large scale genotyping for applications such as WGS in plant breeding.

Modeling of the jasmonate signaling pathway in Arabidopsis thaliana with respect to pathophysiology of Alternaria blight in Brassica

The productivity of Oilseed Brassica, one of the economically important crops of India, is seriously affected by the disease, Alternaria blight. The disease is mainly caused by two major necrotrophic fungi, Alternaria brassicae and Alternaria brassicicola which are responsible for significant yield losses. Till date, no resistant source is available against Alternaria blight, hence plant breeding methods can not be used to develop disease resistant varieties. Jasmonate mediated signalling pathway, which is known to play crucial role during defense response against necrotrophs, could be strengthened in Brassica plants to combat the disease. Since scanty information is available in Brassica-Alternaria pathosystems at molecular level therefore, in the present study efforts have been made to model jasmonic acid pathway in Arabidopsis thaliana to simulate the dynamic behaviour of molecular species in the model. Besides, the developed model was also analyzed topologically for investigation of the hubs node. COI1 is identified as one of the promising candidate genes in response to Alternaria and other linked components of plant defense mechanisms against the pathogens. The findings from present study are therefore informative for understanding the molecular basis of pathophysiology and rational management of Alternaria blight for securing food and nutritional security.

Monsanto gains a CRISPR platform

Monsanto has signed a deal to use the CRISPR/Cas9 gene-editing platform of Seoul, South Korea-based ToolGen to develop products for agriculture. Gene-editing tools can add, delete, or change genes in plants much more quickly than traditional plant breeding and biotechnology methods can, Monsanto says. Monsanto is working to catch up with DuPont Pioneer, the first agricultural company to access CRISPR tools. Early this year Monsanto signed a nonexclusive deal for CRISPR/Cpf1 technology from the Broad Institute of MIT & Harvard.

Characterizing the gut (Gallus gallus) microbiota following the consumption of an iron biofortified Rwandan cream seeded carioca (Phaseolus Vulgaris L.) bean-based diet.

Biofortification is a plant breeding method that introduces increased concentrations of minerals in staple food crops (e.g., legumes, cereal grains), and has shown success in alleviating insufficient Fe intake in various human populations. Unlike other strategies utilized to alleviate Fe deficiency, studies of the gut microbiota in the context of Fe biofortification have not yet been reported, although the consumption of Fe biofortified staple food crops has increased significantly over time. Hence, in this study, we performed a 6-week feeding trial in Gallus gallus (n = 14), aimed to investigate the alterations in the gut microbiome following administration of an Fe biofortified bean-based diet (biofortified, BFe) versus a bean based diet with poorly-bioavailable Fe (standard, SFe). Cream seeded carioca bean based diets were designed in an identical fashion to those used in a recent human clinical trial of Fe biofortified beans in Rwanda. We hypothesized that the different dietary Fe contents in the beans based diets will alter the composition and function of the intestinal microbiome. The primary outcomes were changes in the gut microbiome composition and function analyzed by 16S rRNA gene sequencing. We observed no significant changes in phylogenetic diversity between groups. There were significant differences in the composition of the microbiota between groups, with the BFe group harboring fewer taxa participating in bacterial Fe uptake, increased abundance of bacteria involved in phenolic catabolism, and increased abundance of beneficial butyrate-producing bacteria. Additionally, depletion of key bacterial pathways responsible for bacterial viability and Fe uptake suggest that improvements in Fe bioavailability, in addition to increases in Fe-polyphenol and Fe-phytate complexes due to biofortification, led to decreased concentrations of cecal Fe available for bacterial utilization. Our findings demonstrate that Fe biofortification may improve Fe status without negatively altering the structure and function of the gut microbiota, as is observed with other nutritional methods of Fe supplementation. These results may be used to further improve the efficacy and safety of future biofortification efforts in eradicating global Fe deficiency.

Harnessing Finger Millet to Combat Calcium Deficiency in Humans: Challenges and Prospects.

Humans require more than 20 mineral elements for healthy body function. Calcium (Ca), one of the essential macromineral, is required in relatively large quantities in the diet for maintaining a sound overall health. Young children, pregnant and nursing women in marginalized and poorest regions of the world, are at highest risk of Ca malnutrition. Elderly population is another group of people most commonly affected by Ca deficiency mainly in the form of osteoporosis and osteopenia. Improved dietary intake of Ca may be the most cost-effective way to meet such deficiencies. Finger millet [Eleusine coracana (L.) Gaertn.], a crop with inherently higher Ca content in its grain, is an excellent candidate for understanding genetic mechanisms associated with Ca accumulation in grain crops. Such knowledge will also contribute toward increasing Ca contents in other staple crops consumed on daily basis using plant-breeding (also known as biofortification) methods. However, developing Ca-biofortified finger millet to reach nutritional acceptability faces various challenges. These include identifying and translating the high grain Ca content to an adequately bioavailable form so as to have a positive impact on Ca malnutrition. In this review, we assess some recent advancements and challenges for enrichment of its Ca value and present possible inter-disciplinary prospects for advancing the actual impact of Ca-biofortified finger millet.

Transgenerational Defense Priming for Crop Protection against Plant Pathogens: A Hypothesis.

Throughout evolution, plants have developed diverse mechanisms of defense that “prime” their innate immune system for more robust and active induction of defense responses against different types of stress. Nowadays there are numerous reports concerning the molecular bases of priming, as well as the generational priming mechanisms. Information concerning transgenerational priming, however, remains deficient. Some reports have indicated, nonetheless, that the priming status of a plant can be inherited to its offspring. Here, we show that the priming agent β-aminobutyric acid induced resistance to Pseudomonas syringae pv. phaseolicola infection in the common bean (Phaseolus vulgaris L.) We have analyzed the transgenerational patterns of gene expression of the PvPR1 gene (Phaseolus vulgaris PR1), a highly responsive gene to priming, and show that a transgenerational priming response against pathogen attack can last for at least two generations. We hypothesize that a defense-resistant phenotype and easily identifiable, generational and transgenerational, “primed patterns” of gene expression are excellent indicators of the priming response in crop plants. Furthermore, we propose here that modern plant breeding methods and crop improvement efforts must include the use of elicitors to prime induced resistance in the field and, above all, to select for induced heritable states in progeny that is primed for defense.

Periclinal chimera technique: new plant breeding approach.

Plant interspecific periclinal chimeras are a mosaic formed by tissues from two species. They are manipulated here as an efficient plant breeding tool for cassava root yields. In this study, plants synthesized from two chimeras, designated as chimera 2 and chimera 4, were characterized morphologically and cytologically to unravel the origin of their tissue layers (L2 and L3). Root yield of the two chimeras was also evaluated. Chimera 2 that was developed from graft union between Manihot fortalezensis (F) as scion and M. esculenta (E) as rootstock and the same in chimera 4 was developed from grafting triploid cassava cultivar (2n = 54) (C) as scion and M. pohlii (P) (2n = 36) as rootstock. A new method of inducing interspecific chimeras without using hormones was also tested in this study. Five combinations between four cassava cultivars on one side and M. fortalezensis and an interspecific hybrid (M. glaziovii x M. esculenta) on the other side were experimented to determine compatibility between the parents. Wild species always gave L2 and L3, independent of being used as rootstock or scion. L3 is responsible for producing pericycle. Thus, its performance was different in each chimera due to specific epigenetic interaction. Of 48 grafts, it was obtained one chimera giving a percentage of 2.1% that is little lower than using hormones but much efficient to use. Chimera induction efficiency in this investigation was the same when using hormones. Thus, our new, less labor, and more cost-effective technique is as much efficient as hormones and is much potential to employ as an effective plant breeding method boosting cassava root yield.