Genome-wide association mapping of seed oligosaccharides in chickpea

Abstract

Chickpea (Cicer arietinum L.) is one of the major pulse crops, rich in protein, and widely consumed all over the world. Most legumes, including chickpeas, possess noticeable amounts of raffinose family oligosaccharides (RFOs) in their seeds. RFOs are seed oligosaccharides abundant in nature, which are non-digestible by humans and animals and cause flatulence and severe abdominal discomforts. So, this study aims to identify genetic factors associated with seed oligosaccharides in chickpea using the mini-core panel. We have quantified the RFOs (raffinose and stachyose), ciceritol, and sucrose contents in chickpea using high-performance liquid chromatography. A wide range of variations for the seed oligosaccharides was observed between the accessions: 0.16 to 15.13 mg g-1 raffinose, 2.77 to 59.43 mg g-1 stachyose, 4.36 to 90.65 mg g-1 ciceritol, and 3.57 to 54.12 mg g-1 for sucrose. Kabuli types showed desirable sugar profiles with high sucrose, whereas desi types had high concentrations RFOs. In total, 48 single nucleotide polymorphisms (SNPs) were identified for all the targeted sugar types, and nine genes (Ca_06204, Ca_04353, and Ca_20828: Phosphatidylinositol N-acetylglucosaminyltransferase; Ca_17399 and Ca_22050: Remorin proteins; Ca_11152: Protein-serine/threonine phosphatase; Ca_10185, Ca_14209, and Ca_27229: UDP-glucose dehydrogenase) were identified as potential candidate genes for sugar metabolism and transport in chickpea. The accessions with low RFOs and high sucrose contents may be utilized in breeding specialty chickpeas. The identified candidate genes could be exploited in marker-assisted breeding, genomic selection, and genetic engineering to improve the sugar profiles in legumes and other crop species.

Nutritional profile of chickpea (Cicer arietinum L): Breeding efforts for enhancing nutritive value

“…Kabuli chickpeas were characterized by high sucrose content, while desi types possessed elevated levels of raffinose and stachyose. Genome-wide association studies (GWAS) identified 48 SNPs associated with sugar types, coupled with the identification of nine candidate genes potentially involved in sugar metabolism and transport (Elango et al, 2022). These findings provide valuable insights into the genetic architecture of RFO accumulation in chickpea and lay the groundwork for breeding programs aiming to develop cultivars with reduced anti-nutritional factors and enhanced nutritional value.…”

“…Among RFOs ciceritol exhibited the most significant variation (4.36-90.65 mg/g). Elango et al (2022) further explored this diversity within the chickpea mini-core collection, revealing distinct differences between kabuli and desi biotypes. Kabuli chickpeas were characterized by high sucrose content, while desi types possessed elevated levels of raffinose and stachyose.…”

Unlocking the nutritional potential of chickpea: strategies for biofortification and enhanced multinutrient quality

“…Interestingly, protein contents among commercially cultivated varieties ranged from 18.19-30.44%, relatively lower than germplasm accessions (19.41-33.56%) (Grewal et al, 2023). Farida Traore et al (2022) reported broad variability in SPC (18.9-32.4%) in 282 advanced chickpea breeding lines in Morocco. In another study, SPC varied between desi and kabuli types, with desi types generally lower (20.29%) than kabuli types (24.51%) (Sharma et al, 2013;Ghribi et al, 2015).…”

“…Raffinose and stachyose are galactosyl derivatives of sucrose, with raffinose having one galactose moiety and stachyose having two galactose moieties attached to sucrose via α (1-6) glycosidic linkage ( Chibbar et al., 2010 ; Kaur et al., 2019 ). These compounds are classified as raffinose family oligosaccharides (RFOs), which are non-digestible by humans and animals, often causing flatulence ( Elango et al., 2022 ). Chickpea oligosaccharide levels varied among different cultivars, ranging from 5.54–8.82%, including 0.25–0.73% verbascose, 1.54–3.18% stachyose, 2.04–5.26% ciceritol, and 0.42–0.86% raffinose ( Tosh and Yada, 2010 ; Singh and Kumari, 2011 ).…”

“…The authors identified genes in the QTL regions that encode Fe–S metabolism and Zn-dependent alcohol dehydrogenase activity on CaLG03, Fe ion binding oxidoreductase on CaLG04, and Zn-induced facilitator-like protein and ZIP zinc/iron transport family protein on CaLG05. Whole genome resequencing data identified 48 SNPs associated with targeted sugar types and nine genes “( Ca_06204, Ca_04353 , and Ca_20828 : Phosphatidylinositol N-acetylglucosaminyltransferase ; Ca_17399 and Ca_22050 : Remorin proteins ; Ca_11152 : Protein-serine/threonine phosphatase; Ca_10185, Ca_14209 , and Ca_27229 : UDP-glucose dehydrogenase )” as potential candidates for sugar metabolism and transport in chickpea ( Elango et al., 2022 ). A GWAS using 16,376 single nucleotide polymorphisms (SNP) markers identified seven genomic regions associated with SPC in 336 chickpea accessions, explaining a combined 41% PVE ( Upadhyaya et al., 2016b ) (see Table 3 ).…”