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"Shipe, Emerson"
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Genome-wide association mapping of lentil (Lens culinaris Medikus) prebiotic carbohydrates toward improved human health and crop stress tolerance
by
Agrawal, Shiv Kumar
,
Boatwright, J. Lucas
,
Shipe, Emerson
in
631/208/2491
,
631/208/711
,
631/208/727
2021
Lentil, a cool-season food legume, is rich in protein and micronutrients with a range of prebiotic carbohydrates, such as raffinose-family oligosaccharides (RFOs), fructooligosaccharides (FOSs), sugar alcohols (SAs), and resistant starch (RS), which contribute to lentil's health benefits. Beneficial microorganisms ferment prebiotic carbohydrates in the colon, which impart health benefits to the consumer. In addition, these carbohydrates are vital to lentil plant health associated with carbon transport, storage, and abiotic stress tolerance. Thus, lentil prebiotic carbohydrates are a potential nutritional breeding target for increasing crop resilience to climate change with increased global nutritional security. This study phenotyped a total of 143 accessions for prebiotic carbohydrates. A genome-wide association study (GWAS) was then performed to identify associated variants and neighboring candidate genes. All carbohydrates analyzed had broad-sense heritability estimates (H2) ranging from 0.22 to 0.44, comparable to those reported in the literature. Concentration ranges corresponded to percent recommended daily allowances of 2–9% SAs, 7–31% RFOs, 51–111% RS, and 57–116% total prebiotic carbohydrates. Significant SNPs and associated genes were identified for numerous traits, including a galactosyltransferase (Lcu.2RBY.1g019390) known to aid in RFO synthesis. Further studies in multiple field locations are necessary. Yet, these findings suggest the potential for molecular-assisted breeding for prebiotic carbohydrates in lentil to support human health and crop resilience to increase global food security.
Journal Article
Chickpea (Cicer arietinum L.) as a Source of Essential Fatty Acids – A Biofortification Approach
by
Madurapperumage, Amod
,
Tang, Leung
,
Shipe, Emerson
in
Agricultural production
,
Aroma
,
At risk populations
2021
Chickpea is a highly nutritious pulse crop with low digestible carbohydrates (40–60%), protein (15–22%), essential fats (4–8%), and a range of minerals and vitamins. The fatty acid composition of the seed adds value because fats govern the texture, shelf-life, flavor, aroma, and nutritional composition of chickpea-based food products. Therefore, the biofortification of essential fatty acids has become a nutritional breeding target for chickpea crop improvement programs worldwide. This paper examines global chickpea production, focusing on plant lipids, their functions, and their benefits to human health. In addition, this paper also reviews the chemical analysis of essential fatty acids and possible breeding targets to enrich essential fatty acids in chickpea ( Cicer arietinum ) biofortification. Biofortification of chickpea for essential fatty acids within safe levels will improve human health and support food processing to retain the quality and flavor of chickpea-based food products. Essential fatty acid biofortification is possible by phenotyping diverse chickpea germplasm over suitable locations and years and identifying the candidate genes responsible for quantitative trait loci mapping using genome-wide association mapping.
Journal Article
Field pea (Pisum sativum L.) shows genetic variation in phosphorus use efficiency in different P environments
2020
Field pea is important to agriculture as a nutritionally dense legume, able to fix nitrogen from the atmosphere and supply it back to the soil. However, field pea requires more phosphorus (P) than other crops. Identifying field pea cultivars with high phosphorus use efficiency (PUE) is highly desirable for organic pulse crop biofortification. This study identified field pea accessions with high PUE by determining (1) the variation in P remobilization rate, (2) correlations between P and phytic acid (PA), and (3) broad-sense heritability estimates of P concentrations. Fifty field pea accessions were grown in a completely randomized design in a greenhouse with two replicates under normal (7551 ppm) and reduced (4459 ppm) P fertilizer conditions and harvested at two time points (mid-pod and full-pod). P concentrations ranged from 332 to 9520 ppm under normal P and from 83 to 8473 ppm under reduced P conditions across all tissues and both time points. Field pea accessions showed variation in remobilization rates, with PI 125840 and PI 137119 increasing remobilization of P under normal P conditions. Field pea accessions PI 411142 and PI 413683 increased P remobilization under the reduced P treatment. No correlation was evident between tissue P concentration and seed PA concentration (8–61 ppm). Finally, seed P concentration under limited P conditions was highly heritable (H
2
= 0.85), as was mid-pod lower leaf P concentrations under normal P conditions (H
2
= 0.81). In conclusion, breeding for PUE in field pea is possible by selecting for higher P remobilization accessions in low P soils with genetic and location sourcing.
Journal Article
Organic dry pea (Pisum sativum L.): A sustainable alternative pulse-based protein for human health
by
Agrawal, Shiv Kumar
,
Shipe, Emerson
,
Boatwright, Jon Lucas
in
Amino acids
,
Amino Acids - metabolism
,
Biology and Life Sciences
2023
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.
Journal Article
Organic dry pea (Pisum sativum L.) biofortification for better human health
by
Agrawal, Shiv Kumar
,
Shipe, Emerson
,
Thavarajah, Pushparajah
in
Agricultural production
,
Agriculture
,
Biodiversity
2022
A primary criticism of organic agriculture is its lower yield and nutritional quality compared to conventional systems. Nutritionally, dry pea (Pisum sativum L.) is a rich source of low digestible carbohydrates, protein, and micronutrients. This study aimed to evaluate dry pea cultivars and advanced breeding lines using on-farm field selections to inform the development of biofortified organic cultivars with increased yield and nutritional quality. A total of 44 dry pea entries were grown in two USDA-certified organic on-farm locations in South Carolina (SC), United States of America (USA) for two years. Seed yield and protein for dry pea ranged from 61 to 3833 kg ha-1 and 12.6 to 34.2 g/100 g, respectively, with low heritability estimates. Total prebiotic carbohydrate concentration ranged from 14.7 to 26.6 g/100 g. A 100-g serving of organic dry pea provides 73.5 to 133% of the recommended daily allowance (%RDA) of prebiotic carbohydrates. Heritability estimates for individual prebiotic carbohydrates ranged from 0.27 to 0.82. Organic dry peas are rich in minerals [iron (Fe): 1.9–26.2 mg/100 g; zinc (Zn): 1.1–7.5 mg/100 g] and have low to moderate concentrations of phytic acid (PA:18.8–516 mg/100 g). The significant cultivar, location, and year effects were evident for grain yield, thousand seed weight (1000-seed weight), and protein, but results for other nutritional traits varied with genotype, environment, and interactions. “AAC Carver,” “Jetset,” and “Mystique” were the best-adapted cultivars with high yield, and “CDC Striker,” “Fiddle,” and “Hampton” had the highest protein concentration. These cultivars are the best performing cultivars that should be incorporated into organic dry pea breeding programs to develop cultivars suitable for organic production. In conclusion, organic dry pea has potential as a winter cash crop in southern climates. Still, it will require selecting diverse genetic material and location sourcing to develop improved cultivars with a higher yield, disease resistance, and nutritional quality.
Journal Article
Reaching the highest shelf: A review of organic production, nutritional quality, and shelf life of kale (Brassica oleracea var. acephala)
2021
Societal Impact Statement Since its inception in the early 20th century, organic agriculture has grown increasingly popular due to its focus on a holistic, environmentally friendly approach to crop production. However, it is comparatively limited in biomass production, disease management, nutritional quality, and postharvest treatment compared to conventional agriculture. These challenges carry over into kale production, the majority of which is certified organic. This article reviews organic kale production, morphology, and shelf life, focusing on nutrition and plant breeding. It explores the shortcomings of organic output and potential areas of study to enhance shelf life in organic kale while maintaining nutritional quality. Summary Organic production has grown exponentially over the past few decades in both acreage and popularity worldwide. This review focuses specifically on kale produced in the USA. However, regulations limiting synthetic inputs leave organic produce at a disadvantage compared to conventional agriculture in terms of biomass, nutritional quality, disease management, and postharvest treatment. Organic agriculture requires significant improvements to be a viable means of production for a growing population. Kale (Brassica oleracea var. acephala) is a “nutritional powerhouse” leafy green vegetable. The high concentration of vitamins, minerals, and prebiotic carbohydrates in a low‐calorie food makes kale an important crop for combatting obesity‐related non‐communicable diseases. However, the short shelf life of organic kale and inevitable fresh food waste make developing new kale cultivars with increased shelf life essential. This review article aims to (a) review kale morphology, consumer preference, and production, and (b) review nutritional quality, its effect on shelf life, and current breeding efforts of kale. Future research could focus on developing a kale breeding pipeline following suitable kale germplasm selection adapted to organic agriculture with both superior shelf life and improved nutritional quality. Since its inception in the early 20th century, organic agriculture has grown increasingly popular due to its focus on a holistic, environmentally friendly approach to crop production. However, it is comparatively limited in biomass production, disease management, nutritional quality, and postharvest treatment compared to conventional agriculture. These challenges carry over into kale production, the majority of which is certified organic. This article reviews organic kale production, morphology, and shelf life, focusing on nutrition and plant breeding. It explores the shortcomings of organic output and potential areas of study to enhance shelf life in organic kale while maintaining nutritional quality.
Journal Article
Genome‐wide association studies of nutritional traits in peas (Pisum sativum L.) for biofortification
by
Ballén‐Taborda, Carolina
,
Madurapperumage, Amod
,
Tang, Leung
in
Amino acids
,
Biofortification
,
Chromosome 5
2025
Pea (Pisum sativum L.) is a high‐nutrient, cool‐season legume of increasing relevance in plant‐based nutrition and sustainable agriculture. As demand for alternative protein sources increases, improving pea seeds’ nutritional content and quality through genomics‐assisted breeding has become a priority. Despite its importance, limited research has explored the genetic basis of nutritional traits in pea. In this study, 267 accessions from the United States Department of Agriculture (USDA) Pea Single Plant Plus Collection were evaluated across 3 years at two USDA‐certified organic farms in South Carolina to (1) assess phenotypic variation, (2) characterize the population structure and origin, and (3) perform a genome‐wide association study (GWAS) using 54,316 single‐nucleotide polymorphism markers on five nutritional traits: protein concentration, sulfur‐containing amino acids (SAAs), dietary fiber, total starch, and protein digestibility (PDg). Population structure analysis using ADMIXTURE and principal components analyses identified 10 ancestral subpopulations. GWAS identified 17 marker‐trait associations for protein, SAA, and PDg, including a genomic hotspot on the proximal end of chromosome 5 associated with both protein and SAA. This region harbors candidate genes involved in seed development, germination, and protein biosynthesis, suggesting potential roles in protein and SAAs accumulation. These findings provide valuable insights into the genetic architecture underlying key nutritional traits and highlight candidate target genes for breeding high‐quality, biofortified pea cultivars. This research expands the genetic potential of pea as a sustainable and nutritious crop alternative for plant‐based food systems. Plain Language Summary Peas are cool‐season food legumes that are highly nutritious, whole foods rich in protein, dietary fiber, prebiotic carbohydrates, vitamins, and minerals with low fat content. The objective of this study to evaluate the United States Department of Agriculture (USDA) Pea Single Plant Plus Collection across 3 years at two USDA‐certified organic farms in South Carolina to (1) assess phenotypic variation, (2) characterize the population structure and origin, and (3) perform a genome‐wide association study on five nutritional traits. The results found 17 marker‐trait associations for these five traits. These key genetic markers will be used in future organic pea breeding for plant‐based food systems.
Journal Article
Evaluation of Soybean Germplasm Accessions for Resistance to Phakopsora pachyrhizi Populations in the Southeastern United States, 2009–2012
by
Nelson, Randall L.
,
Harris, Donna K.
,
Boerma, H. Roger
in
Alabama
,
backcrossing
,
Crop diseases
2014
Between 2009 and 2012, 118 soybean [Glycine max (L.) Merr.] accessions from the USDA Soybean Germplasm Collection were screened for resistance to soybean rust (Phakopsora pachyrhizi) at up to five locations in the southeastern United States. In 2009, plant introductions (PIs) from maturity groups III through IX were evaluated for relative disease severity and intensity of sporulation from uredinia compared with 12 susceptible cultivars from the same range of maturity groups. Resistance evaluations were based primarily on disease severity and intensity of sporulation from rust pustules. To assess resistance at several nurseries, a rust index score was calculated from the severity and sporulation ratings. Many of the PIs were moderately to highly resistant at the 2009 locations between Alabama and South Carolina, but the P. pachyrhizi population in Bossier City, LA, was virulent on most of those accessions. The 2011 rating data from Quincy, FL, indicated an increase in the virulence of the pathogen there since 2009, and this trend was observed again in 2012. In contrast, many of the same PIs developed substantially less soybean rust in Attapulgus, GA, in 2012. Despite the comparatively greater disease that many accessions had in Louisiana in 2009 and in Quincy in 2011 and 2012, at least 78 PIs were resistant in Georgia in 2012, and 20 of those were at least moderately resistant in both Florida and Georgia that year. No accessions were immune to rust at all of the nurseries, but PI 200492 (Rpp1), PI 547875 (a backcross line with Rpp1), and PI 567102B (Rpp6) were the most resistant of the accessions with named resistance genes and were among the most resistant accessions overall. Among the most resistant accessions with unknown resistance genes, PI 416826A, PI 417125, PI 567034, and PI 567104B consistently had effective levels of resistance in different locations and years. Information about the most resistant PIs and their reactions to soybean rust infection across years and locations will be useful for the development of rust‐resistant soybean cultivars in the United States.
Journal Article
Effect of Row Spacing and Soybean Genotype on Mainstem and Branch Yield
by
Norsworthy, Jason K.
,
Shipe, Emerson R.
in
agronomy
,
Agronomy. Soil science and plant productions
,
Biological and medical sciences
2005
Partitioning of soybean [Glycine max (L.) Merr.] seed yield between mainstem and branch fractions across row widths and genotypes at recommended seeding rates is not well understood. A field experiment was conducted to evaluate the distribution of seed yield between mainstem and branch fractions of eight soybean genotypes grown in narrow (19 cm) and wide (97 cm) rows at recommended seeding rates. In contrast to adequate rainfall throughout the crop season in 2002, a lack of rainfall during reproductive development in 2003 caused differences in mainstem and branch yield components between years. Mainstem seed yields, averaged over years and genotypes, accounted for 45 and 69% of the total yield in wide and narrow rows, respectively. Mainstem seed yields, averaged over years and row widths, ranged from 62 to 142 g m−2 among genotypes. Ranking of mainstem and branch yields among genotypes was stable over environments. Similarly, row width did not influence mainstem yields among genotypes, but genotype branch yields in wide rows were different from those in narrow rows. Branch seed yields in narrow rows, averaged over years, ranged from 14 to 57% of total seed yield while 47 to 74% of total seed yield was produced on branches in wide rows. This research demonstrates considerable differences exist in mainstem and branch yields among genotypes and that genotypes having superior branch yield should be selected for wide rows while mainstem yield should be used as a selection criteria for narrow rows.
Journal Article
Organic dry pea
by
Boatwright, Lucas
,
Shipe, Emerson
,
Thavarajah, Pushparajah
in
Amino acids
,
Crop yields
,
Health
2023
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.
Journal Article