Metabolomics‐driven gene mining and genetic improvement of tolerance to salt‐induced osmotic stress in maize

Abstract

Summary The farmland of the world’s main corn‐producing area is increasingly affected by salt stress. Therefore, the breeding of salt‐tolerant cultivars is necessary for the long‐term sustainability of global corn production. Previous studies have shown that natural maize varieties display a large diversity of salt tolerance, yet the genetic variants underlying such diversity remain poorly discovered and applied, especially those mediating the tolerance to salt‐induced osmotic stress (SIOS). Here we report a metabolomics‐driven understanding and genetic improvement of maize SIOS tolerance. Using a LC‐MS‐based untargeted metabolomics approach, we profiled the metabolomes of 266 maize inbred lines under control and salt conditions, and then identified 37 metabolite biomarkers of SIOS tolerance (METO1‐37). Follow‐up metabolic GWAS (mGWAS) and genotype‐to‐phenotype modeling identified 10 candidate genes significantly associating with the SIOS tolerance and METO abundances. Furthermore, we validated that a citrate synthase, a glucosyltransferase and a cytochrome P450 underlie the genotype–METO–SIOS tolerance associations, and showed that their favorable alleles additively improve the SIOS tolerance of elite maize inbred lines. Our study provides a novel insight into the natural variation of maize SIOS tolerance, which boosts the genetic improvement of maize salt tolerance, and demonstrates a metabolomics‐based approach for mining crop genes associated with this complex agronomic trait.

The utility of metabolomics as a tool to inform maize biology

“…(2020) Carotenoids in kernels HPLC multiple candidate genes linkage mapping and GWAS Diepenbrock et al. (2020) Anthocyanin in kernels HPLC and spectrophotometry multiple candidate genes GWAS Chatham and Juvik, (2021) Metabolite biomarkers for salt tolerance LC-MS cts3 , cyp709b2 , ugt , and multiple candidate genes GWAS Liang et al. (2021) Abbreviations: a1, anthocyaninless1; bx10a, benzoxazinoneless10a; bx10b, benzoxazinoneless10b; bx10c, benzoxazinoneless10c; c2, colorless2; CEC, cation exchange chromatography; crtRB1 , β-carotene hydroxylase 1; crtRB3 , β-carotene hydroxylase 3; cts3, citrate synthase 3; cyp709b2, cytochrome P450; DGAT1-2, acyl-CoA:diacylglycerol acyltransferase; f3′h1 , flavonoid 3′-hydroxylase; fad2, fatty acid desaturases-2; fatb , acyl-ACP thioesterase; GC, gas chromatography; GC-FID, gas chromatography-flame ionization detector; GRMZM2G008714, pyruvate kinase; GRMZM2G025854, phosphoglucomutase; GRMZM2G039588, glucose-6-phosphate 1-epimerase; GRMZM2G045171, sucrose synthase; GRMZM2G050570, threonine synthase; GRMZM2G051806, hexokinase; GRMZM2G082780, phosphoenolpyruvate carboxylase 4; GRMZM2G088235, urease protein; GRMZM2G110929, GLABRA2 expression modulator; GRMZM2G180625, glyceraldehyde-3-phosphate dehydrogenase; GRMZM2G437912, paralog gene encoding a prephenate dehydratase; GRMZM5G841893, FAD-dependent urate hydroxylase; GRMZM5G852704, ethylene-responsive transcription factor RAP2-4; hggt1, homogentisate geranylgeranyltransferase; LC, liquid chromatography; LC-MS, liquid chromatography-mass spectrometry; lcyE, lycopene epsilon cyclase; NIRS, near-infrared spectroscopy; p, pericarp color; porb2, protochlorophyllide oxidoreductase; psy1 , phytoene synthase 1; QTL, quantitative trait loci; sh2, shrunken2; su1, sugary1; tsp21, terpene synthase21; ugt, glucosyltransferase; vp5, viviparous 5; vte4 , γ-tocopherol methyltransferase; whp1, white pollen1; y1, yellow 1.…”

Associating primary and specialized metabolism with salt induced osmotic stress tolerance in maize

“…Experimental strategy adopted by Liang et al . (2021; pp. 2355–2370) in this issue of New Phytologist .…”

“…In this issue of New Phytologist , Liang et al . (2021; pp. 2355–2370) tackled this complexity by performing a comprehensive metabolite profiling of 266 maize inbred lines and thereby identifying 37 metabolic markers of salt stress tolerance.…”

“…However, despite the considerable success that has been made with the identification of a number of quantitative trait loci regulating Na + homeostasis and tolerance to salt induced osmotic stress, these remain only partially understood most likely due to the complexity of the salt induced osmotic response (Munns & Tester, 2008). In the recently published article in New Phytologist, Liang et al (2021;doi: 10.1111/nph.17323) tackled this complexity by performing a comprehensive metabolite profiling of 266 maize inbred lines and thereby identifying 37 metabolic markers of salt stress tolerance. They subsequently carried out metabolite genome wide association studies (mGWASs), identifying and validating three genes associated with metabolism as playing important roles in this process.…”

“…Fig.1Experimenal strategy adopted byLiang et al (2021; doi: 10.1111/nph.17323) in the recently published article in New Phytologist. Maize seedlings from collections representing 404 or 266 cultivars were analyzed and subjected to salt stress.…”