Evaluating testcross performance and genetic divergence of lines derived from reciprocal tropical maize composites

The development of hybrids with enhanced expression of heterosis depends on the genetic background of the source population and the effectiveness of a breeding scheme used to identify and use divergent inbred lines with good combining ability. The present study was conducted to examine the potential of improved tropical reciprocal composites as sources of inbred lines for developing productive hybrids. Thirty-six S₄ lines derived from the third RRS cycle of each composite were crossed in pairs to form 36 testcrosses, which were evaluated along with commonly grown commercial hybrids in Nigeria across nine test environments. Results showed consistent ranking of testcrosses for grain yield and other traits across the diverse test environments. The best 22 testcrosses produced 21% to 51% more grain yields than the highest yielding commercial hybrid. Several testcrosses combined high grain yields with other desirable agronomic traits. The SSR and SNP markers used in the present study detected a broad range of genetic diversity among the 72 S₄ lines, which was structured along the two composites. The two markers portrayed similar trends in determining genetic distance estimates and detecting composite-specific alleles in the S₄ lines. These results highlight the potential of improved reciprocal composites as sources of new and divergent parents for developing productive hybrids and as sources of novel alleles for broadening and diversifying the genetic base of adapted germplasm to sustain genetic gain in productivity of hybrids in WCA

The Hordeum Toolbox: The Barley Coordinated Agricultural Project Genotype and Phenotype Resource

The use of DNA markers in public sector plant breeding is now the norm. Such markers are common across breeding programs and this commonality enables and enhances collaboration. Therefore, large collaborative research projects that measure several phenotypes across multiple environments coupled with the expanding amount of genotype data attainable with current marker technologies are on the rise and these projects demand efficient data delivery. However, development of computational tools for advanced data integration, visualization, and analysis is still a bottleneck, even though these resources have the greatest potential impact for users who are extracting and developing hypothesis-based solutions. The Hordeum Toolbox (THT) was developed as a data resource for the Barley Coordinated Agricultural Project (CAP) with the novel capability of constructing user-defined downloadable sets of phenotype and/or genotype data for downstream analysis. Internal tools in THT enable users to create clusters of a selected group of lines based on genotype data, parse pedigrees, and select germplasm based on haplotype, phenotype, and agronomic properties. The Hordeum Toolbox can be adapted to breeding programs or collaborations to assist researchers in germplasm selection, genotype data visualization, and the integration of complex data sets for statistical analysisThis is the publisher’s final pdf. The published article is copyrighted by the Crop Science Society of America and can be found at: https://www.crops.org/publications/tp

Advanced health information technologies to engage parents, clinicians, and community nutritionists in coordinating responsive parenting care: Descriptive case series of the women, infants, and children enhancements to early healthy lifestyles for baby (WEE Baby) care randomized controlled trial

Background: Socioeconomically disadvantaged newborns receive care from primary care providers (PCPs) and Women, Infants, and Children (WIC) nutritionists. However, care is not coordinated between these settings, which can result in conflicting messages. Stakeholders support an integrated approach that coordinates services between settings with care tailored to patient-centered needs. Objective: This analysis describes the usability of advanced health information technologies aiming to engage parents in self-reporting parenting practices, integrate data into electronic health records to inform and facilitate documentation of provided responsive parenting (RP) care, and share data between settings to create opportunities to coordinate care between PCPs and WIC nutritionists. Methods: Parents and newborns (dyads) who were eligible for WIC care and received pediatric care in a single health system were recruited and randomized to a RP intervention or control group. For the 6-month intervention, electronic systems were created to facilitate documentation, data sharing, and coordination of provided RP care. Prior to PCP visits, parents were prompted to respond to the Early Healthy Lifestyles (EHL) self-assessment tool to capture current RP practices. Responses were integrated into the electronic health record and shared with WIC. Documentation of RP care and an 80-character, free-text comment were shared between WIC and PCPs. A care coordination opportunity existed when the dyad attended a WIC visit and these data were available from the PCP, and vice versa. Care coordination was demonstrated when WIC or PCPs interacted with data and documented RP care provided at the visit. Results: Dyads (N=131) attended 459 PCP (3.5, SD 1.0 per dyad) and 296 WIC (2.3, SD 1.0 per dyad) visits. Parents completed the EHL tool prior to 53.2% (244/459) of PCP visits (1.9, SD 1.2 per dyad), PCPs documented provided RP care at 35.3% (162/459) of visits, and data were shared with WIC following 100% (459/459) of PCP visits. A WIC visit followed a PCP visit 50.3% (231/459) of the time; thus, there were 1.8 (SD 0.8 per dyad) PCP to WIC care coordin

A communal catalogue reveals Earth's multiscale microbial diversity

Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.Peer reviewe

A communal catalogue reveals Earth’s multiscale microbial diversity

Our growing awareness of the microbial world’s importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial diversity

Genes affecting novel seed constituents in Limnanthes alba Benth: transcriptome analysis of developing embryos and a new genetic map of meadowfoam

The seed oil of meadowfoam, a new crop in the Limnanthaceae family, is highly enriched in very long chain fatty acids that are desaturated at the Δ5 position. The unusual oil is desirable for cosmetics and innovative industrial applications and the seed meal remaining after oil extraction contains glucolimnanthin, a methoxylated benzylglucosinolate whose degradation products are herbicidal and anti-microbial. Here we describe EST analysis of the developing seed transcriptome that identified major genes involved in biosynthesis and assembly of the seed oil and in glucosinolate metabolic pathways. mRNAs encoding acyl-CoA Δ5 desaturase were notably abundant. The library was searched for simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs). Fifty-four new SSR markers and eight candidate gene markers were developed and combined with previously developed SSRs to construct a new genetic map for Limnanthes alba. Mapped genes in the lipid biosynthetic pathway encode 3-ketoacyl-CoA synthase (KCS), Δ5 desaturase (Δ5DS), lysophosphatidylacyl-acyl transferase (LPAT), and acyl-CoA diacylglycerol acyl transferase (DGAT). Mapped genes in glucosinolate biosynthetic and degradation pathways encode CYP79A, myrosinase (TGG), and epithiospecifier modifier protein (ESM). The resources developed in this study will further the domestication and improvement of meadowfoam as an oilseed crop

SlabaughMaryCropSoilSciGenesAffectingNovelSupp6TableS5.xls

The seed oil of meadowfoam, a new crop in the Limnanthaceae family, is highly enriched in very long chain fatty acids that are desaturated at the Δ5 position. The unusual oil is desirable for cosmetics and innovative industrial applications and the seed meal remaining after oil extraction contains glucolimnanthin, a methoxylated benzylglucosinolate whose degradation products are herbicidal and anti-microbial. Here we describe EST analysis of the developing seed transcriptome that identified major genes involved in biosynthesis and assembly of the seed oil and in glucosinolate metabolic pathways. mRNAs encoding acyl-CoA Δ5 desaturase were notably abundant. The library was searched for simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs). Fifty-four new SSR markers and eight candidate gene markers were developed and combined with previously developed SSRs to construct a new genetic map for Limnanthes alba. Mapped genes in the lipid biosynthetic pathway encode 3-ketoacyl-CoA synthase (KCS), Δ5 desaturase (Δ5DS), lysophosphatidylacyl-acyl transferase (LPAT), and acyl-CoA diacylglycerol acyl transferase (DGAT). Mapped genes in glucosinolate biosynthetic and degradation pathways encode CYP79A, myrosinase (TGG), and epithiospecifier modifier protein (ESM). The resources developed in this study will further the domestication and improvement of meadowfoam as an oilseed crop.Keywords: KCS, LPAT, Limnanthes, Desaturase, Meadowfoam, GlucolimnanthinKeywords: KCS, LPAT, Limnanthes, Desaturase, Meadowfoam, Glucolimnanthi

SlabaughMaryCropSoilSciGenesAffectingNovel.pdf

The seed oil of meadowfoam, a new crop in the Limnanthaceae family, is highly enriched in very long chain fatty acids that are desaturated at the Δ5 position. The unusual oil is desirable for cosmetics and innovative industrial applications and the seed meal remaining after oil extraction contains glucolimnanthin, a methoxylated benzylglucosinolate whose degradation products are herbicidal and anti-microbial. Here we describe EST analysis of the developing seed transcriptome that identified major genes involved in biosynthesis and assembly of the seed oil and in glucosinolate metabolic pathways. mRNAs encoding acyl-CoA Δ5 desaturase were notably abundant. The library was searched for simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs). Fifty-four new SSR markers and eight candidate gene markers were developed and combined with previously developed SSRs to construct a new genetic map for Limnanthes alba. Mapped genes in the lipid biosynthetic pathway encode 3-ketoacyl-CoA synthase (KCS), Δ5 desaturase (Δ5DS), lysophosphatidylacyl-acyl transferase (LPAT), and acyl-CoA diacylglycerol acyl transferase (DGAT). Mapped genes in glucosinolate biosynthetic and degradation pathways encode CYP79A, myrosinase (TGG), and epithiospecifier modifier protein (ESM). The resources developed in this study will further the domestication and improvement of meadowfoam as an oilseed crop.Keywords: Meadowfoam, Limnanthes, LPAT, Glucolimnanthin, Desaturase, KCSKeywords: Meadowfoam, Limnanthes, LPAT, Glucolimnanthin, Desaturase, KC