Targeted improvement of plant‐based protein: Genome‐wide association mapping of a lentil (Lens culinaris Medik.) diversity panel

Abstract

Societal Impact StatementThe world is increasingly looking to plant‐based sources to meet its protein needs. Multiple factors are driving this progression, ranging from nutritional and ethical considerations to climate change and population growth. As a pulse crop, lentil is ideal to help meet this change in demand. However, plant‐based proteins have limiting amino acids and lower protein digestibility compared to animal‐based proteins. This research identifies genetic markers that can be used to accelerate breeding of protein quality traits in lentil to ultimately help meet the rising demand in high‐quality plant‐based protein and bolster global food and nutritional security.Summary Lentil (Lens culinaris Medik.) contains ~25% high‐quality protein in addition to high concentrations of prebiotic carbohydrates and micronutrients, such as folate, iron, zinc, and selenium. As animal‐based protein's economic and environmental costs rise, plant‐based protein sources, such as lentil, will become increasingly important to global food systems. Consequently, evaluating and targeting protein quality traits for genomic‐assisted breeding is a valuable objective for lentil breeding programs. A diversity panel of 183 breeding lines was analyzed for protein quality traits, including amino acids and protein digestibility. Genotyping‐by‐sequencing (GBS) data were used to assess population structure and conduct genome‐wide association studies (GWAS). Genes in local linkage disequilibrium (LD) with significant single nucleotide polymorphism (SNP) markers were identified and categorized by homology. Protein quality traits showed a wide range of variation. Repeatability estimates were low to moderate across traits. Twelve traits were strongly correlated with each other (r > .7). Admixture analysis identified six ancestral subpopulations, which also demonstrated clustering in principal component analysis. Ten different traits had significant SNP associations; two loci were shared across multiple traits. Twenty‐seven candidate genes, including glutathione S‐transferase, protease family, and gibberellin 2‐beta‐dioxygenase genes, were identified. This paper identifies SNP markers associated with lentil protein quality traits. Once validated, these SNPs could accelerate lentil protein quality breeding efforts. By targeting lentil's limiting amino acids (methionine and cysteine) and protein digestibility through marker‐assisted selection, the nutritional value of lentil's protein content could be increased without the need to alter total protein content.

Evaluating the breeding potential of cultivated lentils for increasing protein and amino acid concentration in the Northern Great Plains

“…As a complex quantitative trait, protein concentration is controlled by many genes with small effects; consequently, we were able to identify many potential markers for use in local lentil breeding programs (Supplemental Figure 5). In comparison to the results from Johnson et al (2023), we identified only one marker (Lcu.2RBY.Chr5p155854268) within 300 kbp of their QTLs, emphasizing the importance of the environment for identifying markers for breeding purposes. We recommend future studies sample an even broader range of environments to dissect the genes influencing protein concentration.…”

“…Kumar et al (2016) found that both Mediterranean landraces and wild lentil species had higher protein concentration than Indian varieties and breeding lines and, therefore, could be used as a breeding source for increased protein concentration. A diversity panel of cultivated lentil grown under greenhouse conditions had a range of mean total amino acid concentration of 18-36 % with some genetic clusters having higher concentrations of specific amino acids than others (Johnson et al, 2023). In Canada, the smaller red cotyledon lentils tend to show slightly higher protein concentration than the larger yellow cotyledon (green) lentils (Boye et al, 2010;Subedi et al, 2021;Wang, 2022).…”

“…Several GWAS have been conducted to study the genetic association of protein and amino acids in various crops, including soybean (Lee et al, 2019;Zhang et al, 2018;Yuan et al, 2021), chickpea (Karaca et al, 2019), and wheat (Nigro et al, 2019). Johnson et al (2023) recently reported on GWAS results for lentils grown in a greenhouse. Due to the quantitative nature of these traits, however, confirmation through testing across multiple locations and years is recommended.…”

Sustainable Pulse Proteins: Physical, Chemical and Fermentative Modifications

“…), chickpeas (Cicer arietinum L.), common beans (Phaseolus vulgaris L.), lentils (Lens culinaris Medikus) and cowpeas (Vigna unguiculata L. Walp). This is because pulses are high in protein (>20%), dietary fibre and micronutrients, such as folate, iron, zinc, magnesium, potassium and selenium, with <3% fat content [16][17][18][19]. Pulses contain high-quality amino acids distributed proportionately within the different classes, and consequently benefit the consumer nutritionally, therapeutically and techno-functionally.…”