Translational genomics and molecular breeding for enhancing precision and efficiency in crop improvement programs: Some examples in legumes

Legumes like chickpea, pigeonpea and groundnut are protein rich, nutrient-dense, and nitrogen fixing crops. Their importance is increasingly recognized in view of the urgent need to address burgeoning malnutrition problem and to impart sustainability to cropping systems. Breeding programs in these crops have achieved great success. However, consistent improvement in genetic gains demands integration of innovative tools and technologies with crop breeding programs. Genomic resources are of paramount significance in context of improving the efficiency and precision of crop breeding schemes. The last decade has witnessed a remarkable success in generating unprecedented genomic resources in these crops, thus transforming these genomic orphans into genomic resource rich crops. These genomic resources include array-based genotyping platforms, high-resolution genetic linkage maps/HapMaps, comprehensive transcriptome assemblies and gene expression atlas, and whole genome sequences etc. Further progression from the training phase (development) to breeding (deployment) phase is marked with the current availability of a variety of molecular breeding products in these legume crops. In the present review, we discuss how deployment of the modern genomic resources such as next-generation gene discovery techniques and “gold standard experimental designs” is furthering our knowledge about the genetic underpinnings of trait variation. Also, key success stories demonstrating the power of molecular breeding in these legume crops are highlighted. It is opined that the breeding populations constantly improved by sequence-based breeding approach will greatly help improving breeding traits and the genetic gains accruable from crop breeding programs

Boxicity and separation dimension

A family $\mathcal{F}$ of permutations of the vertices of a hypergraph $H$ is called 'pairwise suitable' for $H$ if, for every pair of disjoint edges in $H$, there exists a permutation in $\mathcal{F}$ in which all the vertices in one edge precede those in the other. The cardinality of a smallest such family of permutations for $H$ is called the 'separation dimension' of $H$ and is denoted by $\pi(H)$. Equivalently, $\pi(H)$ is the smallest natural number $k$ so that the vertices of $H$ can be embedded in $\mathbb{R}^k$ such that any two disjoint edges of $H$ can be separated by a hyperplane normal to one of the axes. We show that the separation dimension of a hypergraph $H$ is equal to the 'boxicity' of the line graph of $H$. This connection helps us in borrowing results and techniques from the extensive literature on boxicity to study the concept of separation dimension.Comment: This is the full version of a paper by the same name submitted to WG-2014. Some results proved in this paper are also present in arXiv:1212.6756. arXiv admin note: substantial text overlap with arXiv:1212.675

Interior Weyl-type Solutions of the Einstein-Maxwell Field Equations

Static solutions of the electro-gravitational field equations exhibiting a functional relationship between the electric and gravitational potentials are studied. General results for these metrics are presented which extend previous work of Majumdar. In particular, it is shown that for any solution of the field equations exhibiting such a Weyl-type relationship, there exists a relationship between the matter density, the electric field density and the charge density. It is also found that the Majumdar condition can hold for a bounded perfect fluid only if the matter pressure vanishes (that is, charged dust). By restricting to spherically symmetric distributions of charged matter, a number of exact solutions are presented in closed form which generalise the Schwarzschild interior solution. Some of these solutions exhibit functional relations between the electric and gravitational potentials different to the quadratic one of Weyl. All the non-dust solutions are well-behaved and, by matching them to the Reissner-Nordstr\"{o}m solution, all of the constants of integration are identified in terms of the total mass, total charge and radius of the source. This is done in detail for a number of specific examples. These are also shown to satisfy the weak and strong energy conditions and many other regularity and energy conditions that may be required of any physically reasonable matter distribution.Comment: 21 pages, RevTex, to appear in General Relativity and Gravitatio

Advances in Pigeonpea Genomics

Pigeonpea, a member of family Fabaceae, is one of the important food legumes cultivated in tropical and subtropical regions. Due to its inherent properties to withstand harsh environments, it plays a critical role in ensuring sustainability in the subsistence agriculture. Furthermore, plasticity in the maturity duration imparts it a greater adaptability in a variety of cropping systems. In the post genomics era, the importance of pigeonpea is further evident from the fact that pigeonpea has emerged as first non-industrial legume crop for which the whole genome sequence has been completed. It revealed 605.78 Mb of assembled and anchored sequence as against the predicted 833 Mb genome consequently representing 72.8 % of the whole genome. In order to perform genetic and genomic analysis various molecular markers like random amplified polymorphic DNA (RAPD), restriction fragment length polymorphism (RFLP), amplified fragment length polymorphism (AFLP), simple sequence repeat (SSR), diversity array technology (DArT), single feature polymorphism (SFP), and single nucleotide polymorphism (SNP) were employed. So far four transcriptome assemblies have been constructed and different sets of EST-SSRs were developed and validated in a panel of diverse pigeonpea genotypes. Extensive survey of BAC-end sequences (BESs) provided 3,072 BES-SSRs and all these BES-SSRs were further used for linkage analysis and trait mapping. To make the available linkage information more useful, six intra-specific genetic maps were joined together into a single consensus genetic map providing map positions to a total of 339 SSR markers at map coverage of 1,059 cM. However, earlier very few linkage maps were available in the crop because of non-availability of genomic resources. Several quantitative trait loci (QTLs) associated with traits of agronomic interest including QTLs for sterility mosaic disease, fertility restoration, plant type and earliness have been identified and validated. To strengthen the traditional breeding, plenty of genomics tools and technologies are now available for integration in regular pigeonpea breeding schemes. This article presents the progress made in the area of pigeonpea genomics and outlines its applications in crop breeding for pigeonpea improvement

Genomics and breeding innovations for enhancing genetic gain for climate resilience and nutrition traits

Key message Integrating genomics technologies and breeding methods to tweak core parameters of the breeder’s equation could accelerate delivery of climate-resilient and nutrient rich crops for future food security. Abstract Accelerating genetic gain in crop improvement programs with respect to climate resilience and nutrition traits, and the realization of the improved gain in farmers’ fields require integration of several approaches. This article focuses on innovative approaches to address core components of the breeder’s equation. A prerequisite to enhancing genetic variance (σ2g) is the identification or creation of favorable alleles/haplotypes and their deployment for improving key traits. Novel alleles for new and existing target traits need to be accessed and added to the breeding population while maintaining genetic diversity. Selection intensity (i) in the breeding program can be improved by testing a larger population size, enabled by the statistical designs with minimal replications and high-throughput phenotyping. Selection priorities and criteria to select appropriate portion of the population too assume an important role. The most important component of breeder′s equation is heritability (h2). Heritability estimates depend on several factors including the size and the type of population and the statistical methods. The present article starts with a brief discussion on the potential ways to enhance σ2g in the population. We highlight statistical methods and experimental designs that could improve trait heritability estimation. We also offer a perspective on reducing the breeding cycle time (t), which could be achieved through the selection of appropriate parents, optimizing the breeding scheme, rapid fixation of target alleles, and combining speed breeding with breeding programs to optimize trials for release. Finally, we summarize knowledge from multiple disciplines for enhancing genetic gains for climate resilience and nutritional traits

Reap the crop wild relatives for breeding future crops

Crop wild relatives (CWRs) have provided breeders with several 'game-changing' traits or genes that have boosted crop resilience and global agricultural production. Advances in breeding and genomics have accelerated the identification of valuable CWRs for use in crop improvement. The enhanced genetic diversity of breeding pools carrying optimum combinations of favorable alleles for targeted crop-growing regions is crucial to sustain genetic gain. In parallel, growing sequence information on wild genomes in combination with precise gene-editing tools provide a fast-track route to transform CWRs into ideal future crops. Data-informed germplasm collection and management strategies together with adequate policy support will be equally important to improve access to CWRs and their sustainable use to meet food and nutrition security targets

Exploring behaviors, treatment beliefs, and barriers to oral chemotherapy adherence among adult leukemia patients in a rural outpatient setting

Objective: Adherence to oral chemotherapy is essential for patients with chronic myeloid leukemia (CML) and multiple myeloma (MM) to remain in remission. Few studies have used a Likert-type scale to measure medication adherence in CML and MM patients. We applied a validated treatment adherence tool, the ASK-12 (Adherence Starts with Knowledge®) survey, which assessed inconvenience and forgetfulness, treatment beliefs, and medication-taking behaviors recorded on a five-point Likert-type scale at two visits. Results: A medication adherence survey was administered to 42 newly diagnosed or pre-existing CML or MM patients at two outpatient oncology clinics affiliated with an academic medical center in rural eastern North Carolina. Thirty-one patients completed surveys at visit 1 and visit 2 (median 4.5 months apart). Most patients were treated for MM (65%), were non-Hispanic black (68%) and female (58%). Within subscales, mean adherence scores decreased between visits, signaling better adherence. Overall, visit scores were correlated (0.63, p = 0.001). Forgetting to take medication sometimes was the most common reason for non-adherence. Medication costs were not a barrier for MM patients. Greater patient–provider informed decision-making was identified as an opportunity for quality improvement among CML patients. The ASK-12 survey provided a strategy to obtain robust information on medication adherence

Single feature polymorphisms (SFPs) for drought tolerance in pigeonpea (Cajanus spp.)

Single feature polymorphisms (SFPs) are microarray-based molecular markers that are detected by hybridization of DNA or cRNA to oligonucleotide probes. With an objective to identify the potential polymorphic markers for drought tolerance in pigeonpea [Cajanus cajan (L.) Millspaugh], an important legume crop for the semi-arid tropics but deficient in genomic resources, Affymetrix Genome Arrays of soybean (Glycine max), a closely related species of pigeonpea were used on cRNA of six parental genotypes of three mapping populations of pigeonpea segregating for agronomic traits like drought tolerance and pod borer (Helicoverpa armigiera) resistance. By using robustified projection pursuit method on 15 pair-wise comparisons for the six parental genotypes, 5,692 SFPs were identified. Number of SFPs varied from 780 (ICPL 8755 × ICPL 227) to 854 (ICPL 151 × ICPL 87) per parental combination of the mapping populations. Randomly selected 179 SFPs were used for validation by Sanger sequencing and good quality sequence data were obtained for 99 genes of which 75 genes showed sequence polymorphisms. While associating the sequence polymorphisms with SFPs detected, true positives were observed for 52.6% SFPs detected. In terms of parental combinations of the mapping populations, occurrence of true positives was 34.48% for ICPL 151 × ICPL 87, 41.86% for ICPL 8755 × ICPL 227, and 81.58% for ICP 28 × ICPW 94. In addition, a set of 139 candidate genes that may be associated with drought tolerance has been identified based on gene ontology analysis of the homologous pigeonpea genes to the soybean genes that detected SFPs between the parents of the mapping populations segregating for drought tolerance