Genome-wide identification of xyloglucan endotransglucosylase/hydrolase gene family members in peanut and their expression profiles during seed germination

Abstract

Seed germination marks the beginning of a new plant life cycle. Improving the germination rate of seeds and the consistency of seedling emergence in the field could improve crop yields. Many genes are involved in the regulation of seed germination. Our previous study found that some peanut XTHs (xyloglucan endotransglucosylases/hydrolases) were expressed at higher levels at the newly germinated stage. However, studies of the XTH gene family in peanut have not been reported. In this study, a total of 58 AhXTH genes were identified in the peanut genome. Phylogenetic analysis showed that these AhXTHs, along with 33 AtXTHs from Arabidopsis and 61 GmXTHs from soybean, were classified into three subgroups: the I/II, IIIA and IIIB subclades. All AhXTH genes were unevenly distributed on the 18 peanut chromosomes, with the exception of chr. 07 and 17, and they had relatively conserved exon-intron patterns, most with three to four introns. Through chromosomal distribution pattern and synteny analysis, it was found that the AhXTH family experienced many replication events, including 42 pairs of segmental duplications and 23 pairs of tandem duplications, during genome evolution. Conserved motif analysis indicated that their encoded proteins contained the conserved ExDxE domain and N-linked glycosylation sites and displayed the conserved secondary structural loops 1–3 in members of the same group. Expression profile analysis of freshly harvested seeds, dried seeds, and newly germinated seeds using transcriptome data revealed that 26 AhXTH genes, which account for 45% of the gene family, had relatively higher expression levels at the seed germination stage, implying the important roles of AhXTHs in regulating seed germination. The results of quantitative real-time PCR also confirmed that some AhXTHs were upregulated during seed germination. The results of GUS histochemical staining showed that AhXTH4 was mainly expressed in germinated seeds and etiolated seedlings and had higher expression levels in elongated hypocotyls. AhXTH4 was also verified to play a crucial role in the cell elongation of hypocotyls during seed germination.

Genome-wide characterization of the xyloglucan endotransglucosylase/hydrolase gene family in Solanum lycopersicum L. and gene expression analysis in response to arbuscular mycorrhizal symbiosis

“…Furthermore, based on the release of the tomato genome ( The Tomato Genome Consortium, 2012 ), we identified 37 SlXTH gene members by genome-wide screening. Consistent with this, large numbers of XTHs have been found in other plant species ( Yokoyama & Nishitani, 2001 ; Yokoyama, Rose & Nishitani, 2004 ; Saladié et al, 2006 ; Atkinson et al, 2009 ; Rai et al, 2016 ; Song et al, 2018 ; Wang et al, 2018 ; Fu, Liu & Wu, 2019 ; Li et al, 2019 ; Wu et al, 2020 ; Zhu et al, 2022 ; Qiao et al, 2022 ; Yang, Zhang & Zhou, 2022 ).…”

“…Three SlXTHs (SlXTH30, SlXTH31, and SlXTH36) clustered into this family, whereas the rest of the SlXTH members grouped into the I/II subfamily, which includes most of the XTHs from A. thaliana predominantly exhibiting XET activity ( Rose et al, 2002 ). All these results suggest that structural characteristics in the amino acid sequence of each XTH protein might result in a high possibility of functioning as XEH instead of XET and support the idea that XTH proteins might cluster according to their functional activity in different plants ( Song et al, 2018 ; Wang et al, 2018 ; Fu, Liu & Wu, 2019 ; Li et al, 2019 ; Wu et al, 2020 ; Zhu et al, 2022 ; Qiao et al, 2022 ; Yang, Zhang & Zhou, 2022 ). Additional studies are needed to confirm whether each subfamily of the SlXTH protein family has XEH, XET, or combined functions.…”

“…Our study shows that most SlXTH gene duplicated pairs present common cis -acting regulatory elements in their promoter region. Regulatory elements play essential roles by modulating the transcriptional gene expression ( Zhu et al, 2022 ). This study found various phytohormone and defense/stress-responsive elements in the promoter regions of SlXTH genes, including MeJa-responsive and W-box elements, essential factors regulating plant responses to abiotic and biotic stresses.…”

“…Different numbers of XTH genes have been identified and characterized in plant species such as Arabidopsis thaliana (33 genes; Yokoyama & Nishitani, 2001 ), Oryza sativa (29 genes; Yokoyama, Rose & Nishitani, 2004 ), Sorghum bicolor (35 genes; Rai et al, 2016 ), Hordeum vulgare (24 genes; Fu, Liu & Wu, 2019 ), Actinidia deliciosa (14 genes; Atkinson et al, 2009 ), Malus domestica (11 genes; Atkinson et al, 2009 ), Glycine max (61 genes; Song et al, 2018 ), Solanum lycopersicum (25 genes; Saladié et al, 2006 ), Ananas comosus (48 genes; Li et al, 2019 ), Brassica rapa (53 genes; Wu et al, 2020 ), Brassica oleracea (38 genes; Wu et al, 2020 ), Nicotiana tabacum (56 genes; Wang et al, 2018 ), Vitis vinifera L. (34 genes; Qiao et al, 2022 ), Arachis hypogaea L. (58 genes; Zhu et al, 2022 ) and Schima superba (34 genes; Yang, Zhang & Zhou, 2022 ).…”

Gene expression profiling of soaked dry beans (Phaseolus vulgaris L.) reveals cell wall modification plays a role in cooking time

“…Enzymes controlling plant development like tetraspanin 8, early nodulin‐related, and WUS‐interacting protein 2 as well as cell wall modification enzymes like XTH and EXPA1 were upregulated in TZ‐27 in response to abiotic stress, but the upregulation of these genes can also lead to cell wall modifications in legumes during germination (Zhu et al., 2022). This finding appears to contradict previous findings that actively expanding cell walls are more pliable and easier to break down than nonactively expanding cell walls.…”