Genome‐wide association studies of nutritional traits in peas (Pisum sativum L.) for biofortification

In proclaiming the week of August 23–29 National Community Gardening Week, Agriculture Secretary Tom Vilsack noted, “Community gardens provide numerous benefits including opportunities for local food production, resource conservation, and neighborhood beautification. But they also promote family and community interaction and enhance opportunities to eat healthy, nutritious foods. Each of these benefits is something we can and should strive for.” Vilsack’s statement was the latest in a string of signals in the past 7 months that suggest significant changes are afoot at the U.S. Department of Agriculture (USDA). On 29 July 2009 Agriculture Deputy Secretary Kathleen Merrigan inaugurated a new rooftop garden at the offices of the USDA Economic Research Service. In early spring, Vilsack “broke pavement” for a vegetable garden known as the People’s Garden, which was planted in front of USDA headquarters across from the National Mall. And a March 2009 planning meeting to discuss the People’s Garden and other sustainability initiatives, chaired by Vilsack, included people not typically seen at USDA meetings in the past: representatives from community garden associations, local food policy councils, botanical gardens, and the Rodale Institute, a nonprofit organization in Pennsylvania dedicated to organic farming research. Vilsack “talked about sustainability, linking agriculture, food, and human health in a way that you haven’t heard [from USDA],” recalls Rose Hayden-Smith, a fellow at the Minneapolis-based nonprofit Institute for Agriculture and Trade Policy and master gardener for the California Cooperative Extension service.

Integration of genome-wide association and genomic prediction for dissecting seed protein and amino acid in foxtail millet

Genome-wide association study (GWAS) was conducted to identify loci associated with agronomic (days to flowering, days to maturity, plant height, seed yield and seed weight), seed morphology (shape and dimpling), and seed quality (protein, starch, and fiber concentrations) traits of field pea (Pisum sativum L.). A collection of 135 pea accessions from 23 different breeding programs in Africa (Ethiopia), Asia (India), Australia, Europe (Belarus, Czech Republic, Denmark, France, Lithuania, Netherlands, Russia, Sweden, Ukraine and United Kingdom), and North America (Canada and USA), was used for the GWAS. The accessions were genotyped using genotyping-by-sequencing (GBS). After filtering for a minimum read depth of five, and minor allele frequency of 0.05, 16,877 high quality SNPs were selected to determine marker-trait associations (MTA). The LD decay (LD1/2max,90) across the chromosomes varied from 20 to 80 kb. Population structure analysis grouped the accessions into nine subpopulations. The accessions were evaluated in multi-year, multi-location trials in Olomouc (Czech Republic), Fargo, North Dakota (USA), and Rosthern and Sutherland, Saskatchewan (Canada) from 2013 to 2017. Each trait was phenotyped in at least five location-years. MTAs that were consistent across multiple trials were identified. Chr5LG3_566189651 and Chr5LG3_572899434 for plant height, Chr2LG1_409403647 for lodging resistance, Chr1LG6_57305683 and Chr1LG6_366513463 for grain yield, Chr1LG6_176606388, Chr2LG1_457185, Chr3LG5_234519042 and Chr7LG7_8229439 for seed starch concentration, and Chr3LG5_194530376 for seed protein concentration were identified from different locations and years. This research identified SNP markers associated with important traits in pea that have potential for marker-assisted selection towards rapid cultivar improvement.

The present study entitled “Line × Tester analysis in garden pea” was undertaken to estimate the extent of heterosis and combining ability effects for growth, yield and quality traits in pea. Experimental materials comprise five lines viz., Arka Uttam, IIHR-48, IIHR-34, IIHR-41, Arka Tapas and three testers viz., Arka Ajith, Arka Sampoorna and Arka Priya with their fifteen crosses along with one check Arka Pramodh. The parents and hybrids were randomized separately and sown using a Randomized Block Design with two replications during 2019-20. The results revealed that the female parent Arka Tapas recorded a significant GCA effect for most growth and yield parameters. The cross Arka Tapas × Arka Priya exhibited a high percentage of mid-parent (38.74 %), better parent (16.70 %) and heterosis over the commercial check (9.96 %) for the character pod yield per hectare.

Construction of a high-resolution genetic map of Crassostrea gigas: QTL mapping and GWAS applications revealed candidate genes controlling nutritional traits

Background: A study was carried out to estimate the general and specific combining abilities, as well as heterosis for seed yield and yield associated traits in pea lines. Methods: Twenty-eight cross combinations were generated using half-diallel mating design with eight parental lines. The mean values of seed yield and its contributing traits of parental lines and their offspring for each replication were used for statistical analysis viz., GCA, SCA and Heterosis. Result: The GCA and SCA were significant and indicating the presence of both additive and non-additive types of gene actions. AP-3, VL-7, Kashi_Nandini and PC-531 were identified as promising parents due to significant GCA effects on seed yield and other traits. Among the crosses Kashi_Nandini x PC-531, VL-7 x PMR-53, Arkel x Vl-7 and VL-7 x Kashi_uday hybrids were the most promising, with significantly higher SCA effects for seed yield and yield related traits. Seed yield showed significantly high heterosis ranged from -2.00% to 8.77 % (AP-3 x PC-531 and Arkel x PMR-53, respectively) and relative heterosis ranged from -0.75% to 14.10% (Kashi_uday x PC-531 and Arkel x PMR-53 respectively) significantly exhibited positive heterosis for seed yield over better parent and mid-parent.

Digestibility of protein in traditional diets from developing countries such as India, Guatemala, and Brazil is considerably lower compared to that of protein in typical North American diets (54-78 versus 88-94%). The presence of less digestible protein fractions, high levels of insoluble fiber, and high concentrations of antinutritional factors in the diets of developing countries, which are based on less refined cereals and grain legumes as major sources of protein, are responsible for poor digestibility of protein. The effects of the presence of some of the important antinutritional factors on protein and amino digestibilities of food and feed products are reviewed in this chapter. Food and feed products may contain a number of antinutritional factors that may adversely affect protein digestibility and amino acid availability. Antinutritional factors may occur naturally, such as glucosinolates in mustard and rapeseed protein products, trypsin inhibitors and hemagglutinins in legumes, tannins in legumes and cereals, phytates in cereals and oilseeds, and gossypol in cottonseed protein products. Antinutritional factors may also be formed during heat/alkaline processing of protein products, yielding Maillard compounds, oxidized forms of sulfur amino acids, D-amino acids, and lysinoalanine (LAL, an unnatural amino acid derivative). The presence of high levels of dietary trypsin inhibitors from soybeans, kidney beans, or other grain legumes can cause substantial reductions in protein and amino acid digestibilities (up to 50%) in rats and pigs. Similarly, the presence of high levels of tannins in cereals, such as sorghum, and grain legumes, such as fababean (Vicia faba L.), can result in significantly reduced protein and amino acid digestibilities (up to 23%) in rats, poultry, and pigs. Studies involving phytase supplementation of production rations for swine or poultry have provided indirect evidence that normally encountered levels of phytates in cereals and legumes can reduce protein and amino acid digestibilities by up to 10%. D-amino acids and LAL formed during alkaline/heat treatment of proteins such as casein, lactalbumin, soy protein isolate, or wheat proteins are poorly digestible (less than 40%), and their presence can reduce protein digestibility by up to 28% in rats and pigs. A comparison of the protein digestibility determination in young (5-week) versus old (20-month) rats suggests greater susceptibility to the adverse effects of antinutritional factors in old rats than in young rats. Therefore, the inclusion of protein digestibility data obtained with young rats, as the recommended animal model, in the calculation of PDCAAS (Protein Digestibility-Corrected Amino Acid Score) may overestimate protein digestibility and quality of products, especially those containing antinutritional factors, for the elderly. For products specifically intended for the elderly, protein digestibility should be determined using more mature rats.

The testa layer of sorghum [Sorghum bicolor (L.) Moench] seed plays an important role in the digestion and assimilation of grain protein and amino acids. We studied the relationship of the testa character to agronomic and nutritional traits (including two minerals) in S1 families from two random‐mating populations, NP13R (diverse germplasm) and NP14B (narrow base), where each was divided into subpopulations with and without a testa layer. In 1976, 200 families from each subpopulation were tested, and in 1977, 160 families from each were used.Differences occurred between the testa and nontesta subpopulations in at least one population in at least 1 year for all of the traits studied except grain yield and height. The testa types tended to have lower means for other agronomic traits, although differences were not always significant. Among the nutritional and mineral traits, the testa types had more protein, lysine percent sample, K, and tannin; and less lysine percent protein, oil, carbohydrate, P, gross energy, enzyme (α‐amylase) activity, in vitro dry matter digestibility, and metabolizable energy than the nontesta types. However, the results were highly influenced by the environment.Correlations among traits were similar, with the exception of correlations involving tannin and enzyme activity, in each subpopulation. Tannin and enzyme activity were correlated with the other traits at similar magnitudes but of opposite sign when comparisons were made between the testa and nontesta subpopulations within each population.Comparisons of mean values and the correlations of tannin and enzyme activity with the other traits indicated that the nontesta genotypes did not contain any astringent polyphenols although variable amounts of phenolic compounds were measured. Among the testa genotypes, astringent polyphenols were found in some S1 families but not others. Their tannin level and inhibitory effect on amylase activity were variable and greatly influenced by environment.

Aquaculture relies significantly on fish meal and fish oil, which are abundant in proteins, amino acids and fatty acids; nevertheless, their elevated costs, raw material requirements, and environmental issues have necessitated the exploration of alternative protein sources. Black Soldier Fly Larvae (BSFL) have surfaced as a feasible alternative to fish meal owing to their analogous nutritional composition, especially their protein levels, rendering them a cost-efficient and sustainable choice in aquafeeds. BSFL grow in decaying organic materials and have been employed for waste management in commercial swine and poultry industries. Their life cycle, characterised by the effective transformation of waste into protein, amplifies their significance in sustainable agriculture. This study aimed to evaluate proximate composition of BSFL produced from household waste. The proximate analysis of the BSFL samples indicated a moisture content of 54.78±0.02%, a protein content of 45.29±0.52%, a lipid content of 4.12±0.01%, and an ash content of 9.03±0.02%. There were significant difference in moisture, protein, fat, and ash content among all diets (p < 0.05), with BSFL having the highest values in all components. BSFL's high protein concentration makes it a prospective alternative protein source for aquaculture, while its balanced composition suggests that it could be used a variety of animal feed applications. The study emphasizes the importance of optimizing BSFL diets to improve their nutritional content and promote sustainable farming practices, particularly in light of the growing demand for alternative protein sources.

Perspectives on the genetic improvement of health- and nutrition-related traits in pea

How the USDA School Meal Guidelines Impact Fruits and Vegetables Selection and Waste in School Cafeterias

Dry pea (Pisum sativum L.) is a cool-season food legume rich in protein (20–25%). With increasing health and ecosystem awareness, organic plant-based protein demand has increased; however, the protein quality of organic dry pea has not been well studied. This study determined the genetic variation of individual amino acids (AAs), total AAs (liberated), total protein, and in vitro protein digestibility of commercial dry pea cultivars grown in organic on-farm fields to inform the development of protein-biofortified cultivars. Twenty-five dry pea cultivars were grown in two USDA-certified organic on-farm locations in South Carolina (SC), USA, for two years (two locations in 2019 and one in 2020). The concentrations of most individual AAs (15 of 17) and the total AA concentration significantly varied with dry pea cultivar. In vitro protein digestibility was not affected by the cultivar. Seed total AA and protein for dry pea ranged from 11.8 to 22.2 and 12.6 to 27.6 g/100 g, respectively, with heritability estimates of 0.19 to 0.25. In vitro protein digestibility and protein digestibility corrected AA score (PDCAAS) ranged from 83 to 95% and 0.18 to 0.64, respectively. Heritability estimates for individual AAs ranged from 0.08 to 0.42; principal component (PCA) analysis showed five significant AA clusters. Cultivar Fiddle had significantly higher total AA (19.6 g/100 g) and digestibility (88.5%) than all other cultivars. CDC Amarillo and Jetset were significantly higher in cystine (Cys), and CDC Inca and CDC Striker were significantly higher in methionine (Met) than other cultivars; CDC Spectrum was the best option in terms of high levels of both Cys and Met. Lysine (Lys) concentration did not vary with cultivar. A 100 g serving of organic dry pea provides a significant portion of the recommended daily allowance of six essential AAs (14–189%) and daily protein (22–48%) for an average adult weighing 72 kg. Overall, this study shows organic dry pea has excellent protein quality, significant amounts of sulfur-containing AAs and Lys, and good protein digestibility, and thus has good potential for future plant-based food production. Further genetic studies are warranted with genetically diverse panels to identify candidate genes and target parents to develop nutritionally superior cultivars for organic protein production.

Dry pea (Pisum sativum L.) is a cool-season food legume rich in protein (20-25%). With increasing health and ecosystem awareness, organic plant-based protein demand has increased; however, the protein quality of organic dry pea has not been well studied. This study determined the genetic variation of individual amino acids (AAs), total AAs (liberated), total protein, and in vitro protein digestibility of commercial dry pea cultivars grown in organic on-farm fields to inform the development of protein-biofortified cultivars. Twenty-five dry pea cultivars were grown in two USDA-certified organic on-farm locations in South Carolina (SC), USA, for two years (two locations in 2019 and one in 2020). The concentrations of most individual AAs (15 of 17) and the total AA concentration significantly varied with dry pea cultivar. In vitro protein digestibility was not affected by the cultivar. Seed total AA and protein for dry pea ranged from 11.8 to 22.2 and 12.6 to 27.6 g/100 g, respectively, with heritability estimates of 0.19 to 0.25. In vitro protein digestibility and protein digestibility corrected AA score (PDCAAS) ranged from 83 to 95% and 0.18 to 0.64, respectively. Heritability estimates for individual AAs ranged from 0.08 to 0.42; principal component (PCA) analysis showed five significant AA clusters. Cultivar Fiddle had significantly higher total AA (19.6 g/100 g) and digestibility (88.5%) than all other cultivars. CDC Amarillo and Jetset were significantly higher in cystine (Cys), and CDC Inca and CDC Striker were significantly higher in methionine (Met) than other cultivars; CDC Spectrum was the best option in terms of high levels of both Cys and Met. Lysine (Lys) concentration did not vary with cultivar. A 100 g serving of organic dry pea provides a significant portion of the recommended daily allowance of six essential AAs (14-189%) and daily protein (22-48%) for an average adult weighing 72 kg. Overall, this study shows organic dry pea has excellent protein quality, significant amounts of sulfur-containing AAs and Lys, and good protein digestibility, and thus has good potential for future plant-based food production. Further genetic studies are warranted with genetically diverse panels to identify candidate genes and target parents to develop nutritionally superior cultivars for organic protein production.

Food and nutritional security are an essential goals for the entire global population during climate change scenarios. These twin challenges can be addressed by expanding the global cropping system by promoting grain and legume crops, especially pulses in India. Legume seeds are known as “meat for vegetarian diets”. Ever-increasing pigeonpea consumption as a major source of protein necessitates the improvement of varieties for more efficient production. Pigeonpea is an important legume crop with high protein content and nutritional attributes for more than a billion people living in South Asia. This hardy legume has a considerable potential positive impact on the lives of poor farmers as compared to other legumes, due to better productivity under extreme environmental conditions such as heat, drought and low soil fertility. However, pigeonpea productivity is still low for decades because of sparse utilization of landraces and wild pigeonpea germplasm as genetic and genomic resources. Recent advances in next-generation sequencing, together with other “omics” technologies have significantly reinforced pigeonpea research. Despite the remarkable progress in these technologies, the analysis and mining of existing seed genomics data are still challenging due to the complexity of genetic inheritance, metabolic partitioning, and developmental regulations. The integration of “omics tools” is an effective strategy to discover critical regulators of various seed traits. To utilize its potential, a coordinated and comprehensive evaluation of germplasm is required. Identification of potential genes/alleles governing complex traits of seed quality and nutritional content such as seed weight, seed size, seed color, total protein content, amino acid, antioxidant, resistant starch and disease resistance are essential in genomic selection for quality trait improvement of pigeonpea. Therefore, we need to understand these complex genetic architectures of qualitative and quantitative traits in pigeonpea for the development of nutrient-dense varieties for value addition. It helps in reducing malnutrition, protein, energy, and amino acid deficiency in food and feed related problems that are common in the majority of the population and more specific to developing countries. In this review, a comprehensive discussion on recent advances in “omics” approaches, their use in pigeonpea seed quality, and nutritional trait investigations are presented along with the available databases and technological platforms and their applicability in the improvement of pigeonpea. This article highlights the catalog of important available resources to improve the knowledge base and its future utilization in pigeonpea crop improvement programs.

Exploration of the Genetic Basis of GVHD by Genetic Association Studies