Haplotype shifts in the lipid-related OsGELP gene family underpin rice adaptation to high latitudes

Abstract

Rice (Oryza sativa L.) originated in tropical regions but has successfully adapted to higher latitudes, largely through modifications in photoperiod sensitivity and cold tolerance mechanisms. Lipid metabolism, particularly involving membrane-associated enzymes, plays a key role in environmental sensing and response. The GDSL esterase/lipase (GELP) gene family, known for its lipid-related enzymatic activity, has been associated with various abiotic stress responses. In this study, we investigated the potential role of OsGELP genes in rice adaptation to high-latitude environments using publicly available genomic and geolocation data from 3,000 rice accessions. We identified haplotypes for all 115 OsGELP genes and classified them based on single-nucleotide polymorphisms (SNPs) and the mean latitude of occurrence. Haplotypes with average latitudinal distribution above 35°N were defined as high-latitude haplotypes (HLHs). We selected 10 OsGELP genes containing 11 HLHs for further analysis. Haplotype network and amino acid sequence analyses revealed that a limited number of non-synonymous mutations in HLHs may have conferred adaptive advantages to high-latitude environments. Notably, these HLH-associated OsGELP genes are predominantly expressed in roots, suggesting a root-mediated mechanism of environmental adaptation. Interestingly, only 3 of 14 known cold tolerance genes in rice exhibited HLHs, highlighting the distinct role of OsGELP genes in latitude adaptation. Our findings suggest that these 10 OsGELP genes with HLHs may represent previously unrecognized genetic components contributing to high-latitude adaptation in rice.

Keywords: OsGELP; Adaptation; GDSL-type esterase/lipase; High-latitude haplotype; Rice; Root.

Fig. 1

Workflow of general and specific analyses of identification 115 OsGELP genes related to latitude across 3000 RG.

Fig. 2

GLA in 12 OsGELP genes. A. OsGELP4; B. OsGELP18; C. OsGELP19; D. OsGELP42; E. OsGELP58; F. OsGELP60; G. OsGELP64; H. OsGELP65; I. OsGELP66; J. OsGELP90; K. OsGELP104; L. OsGELP107. Blue dots, Japanese accessions; red dots, Indonesian accessions. Different letters indicate significant differences based on Duncan’s test (p < 0.05). Haplotype identified in more than 30 accessions from the 3000 rice genomes were considered for analysis.

Fig. 3

SLA in ten HLH genes. A. OsGELP4; B. OsGELP18; C. OsGELP19; D. OsGELP42; E. OsGELP58; F. OsGELP60; G. OsGELP64; H. OsGELP65; I. OsGELP66; J. OsGELP90; K. OsGELP104; L. OsGELP107. Blue dots, Japanese accessions; red dots, Indonesian accessions. The y axis shows the latitude average in each haplotype. Different letters indicate significant differences based on Duncan’s test (p < 0.05). Haplotypes identified in more than 30 accessions from the 3000 rice genomes were considered for analysis.

Fig. 4

Presence of HLH in ten HLH genes in Hokkaido rice varieties. Grey box shows the HLH and number in x and y axis are the total number of HLH.

Fig. 5

Haplotype networks of ten HLH genes. A. OsGELP18; B. OsGELP19; C. OsGELP42; D. OsGELP58; E. OsGELP60; F. OsGELP64; G. OsGELP65; H. OsGELP66; I. OsGELP90; and J. OsGELP107. Haplotypes are represented by circles, where the size of each circle show the proportion to the frequency of the corresponding haplotype. Lines on connecting branches represent mutation in SNP. Each circle represents a haplotype, with the size proportional to the number of samples sharing in the haplotypes (circle scale 10 to 1 samples or accession). Colors within each circle correspond to different rice subpopulations, as indicated in the legend (e.g., admix, aus, indica, japonica subgroups, subtropical, temperate, tropical). Red dashed boxes highlight haplotypes associated with cold tolerance (HLH).

Fig. 6

Comparisons of nucleotide and amino acid variations in the HLH genes OsGELP18, OsGELP19, and OsGELP64. A. Haplotype variation of OsGELP18 in 22 Hokkaido varieties and three additional cultivars. Yellow rows indicate HLH varieties. SNP positions on Chr. 1 are: [1 = 26,200,500; 2 = 26,200,740; 3 = 26,200,744; 4 = 26,200,829; 5 = 26,200,859; 6 = 26,200,980; 7 = 26,201,066]. Haplotype 7 contains a “TA” insertion at position 26,201,067 relative to the Nipponbare reference (“nf”: not found). Among the 22 Hokkaido varieties, 18 carried HLH-type haplotypes. A polymorphic amino acid site at position 291 shows glutamic acid (E) in haplotypes 3 and 7 (non-HLH, red arrow, lower-latitude accessions) and lysine (K) in haplotype 26 and Nipponbare (HLH, blue arrow, higher-latitude accessions). B. Haplotype variation of OsGELP19 in 22 Hokkaido varieties and six additional cultivars. Yellow rows indicate HLH varieties. SNP positions on Chr. 1 are: [1 = 26,203,092; 2 = 26,203,969; 3 = 26,204,143; 4 = 26,204,442; 5 = 26,205,695; 6 = 26,205,789; 7 = 26,206,196]. Haplotype 83 contains a “CACGTTCGCT” insertion at position 26,206,197 relative to the Nipponbare reference. Among the 22 Hokkaido varieties, 17 carried HLH-type haplotypes. A polymorphic amino acid site at position 414 shows phenylalanine (F) in haplotypes 811 and 7 (non-HLH, red arrow, lower latitudes) and leucine (L) in haplotype 646 and Nipponbare (HLH, blue arrow, higher latitudes). C. Haplotype variation of OsGELP64 in 22 Hokkaido varieties and six additional cultivars. Yellow rows indicate HLH varieties. SNP positions on Chr. 5 are: [1 = 6,825,409; 2 = 6,825,625; 3 = 6,825,647; 4 = 6,825,677; 5 = 6,825,698; 6 = 6,825,714; 7 = 6,825,793; 8 = 6,825,867; 9 = 6,826,118; 10 = 6,826,745; 11 = 6,826,769; 12 = 6,827,210]. Among the 22 Hokkaido varieties, 17 carried HLH-type haplotypes. D. Amino acid variation in OsGELP64 haplotypes. Polymorphic sites are located at position 122 (alanine [A] in HLH haplotype 200 and Nipponbare vs valine [V] in non-HLH haplotypes 1, 81, 261, 72, and 167) and position 326 (histidine [H] in HLH haplotype 200 and Nipponbare vs arginine [R] in non-HLH haplotypes). In addition, haplotype 167 carries threonine (T) at position 415, while others have isoleucine (I). Red arrows indicate non-HLH haplotypes, and blue arrows indicate HLH haplotypes. E. Predicted protein 3D structural differences between HLH-type haplotype 200 and non-HLH-type haplotype 81 of OsGELP64 (AlphaFold DB). The polymorphism at amino acid position 122 (A↔V) alters the arrangement of α-helices (spirals) and β-sheets (green). Numbers in parentheses indicate the average latitude of each haplotype.