锦葵科植物果胶酸裂解酶（PEL）基因家族的全基因组鉴定及其对棉花纤维品质的影响

doi:10.1016/j.jia.2024.06.011

摘要/Abstract

摘要：

果胶是植物细胞壁的主要组成成分之一。果胶酸裂解酶通过 β-消除作用随机切割 α 1,4-糖苷键，产生不饱和的4,5-低聚半乳糖醛酸，导致同聚半乳糖醛酸解聚。然而，有关锦葵科植物中果胶酸裂解酶基因家族的进化与比较分析的研究十分有限。本研究从10个锦葵科植物中鉴定到了597个非冗余的PEL基因家族成员。系统发育树和保守基序分析结果显示，PEL基因家族可分为六个亚家族，分别是：Clade I、II、III、IV、Va和Vb。其中，亚家族Clade I和II中的成员数量最多，分别为237和222个成员。Clade Va和Vb亚家族的PEL基因只包含四到五个Motif，比其他亚家族要少得多。棉花中PEL家族成员主要通过片段复制事件进行扩增。陆地棉和海岛棉中，Clade I、IV、Va和Vb亚家族成员在棉纤维伸长阶段具有较高的表达水平，Clade II和III亚家族中几乎所有PEL成员在本研究中检测的所有纤维发育阶段都没有表达量。在陆地棉和海岛棉群体中通过单基因关联分析，鉴定到14个与纤维长度和强度性状显著相关的GbPELs，而在陆地棉群体中，仅鉴定到8个GhPEL基因与纤维品质性状显著关联。本研究对PEL基因进行全基因组鉴定和比较分析，为该基因在棉纤维品质改良中的潜在利用价值提供了重要支撑。

Abstract:

Pectin is a major constituent of the plant cell wall. Pectate lyase (PEL, EC 4.2.2.2) uses anti-β-elimination chemistry to cleave the α-1,4 glycosidic linkage in the homogalacturonan region of pectin. However, limited information is available on the comprehensive and evolutionary analysis of PELs in the Malvaceae. In this study, we identified 597 PEL genes from 10 Malvaceae species. Phylogenetic and motif analyses revealed that these PELs are classified into six subfamilies: Clades I, II, III, IV, Va, and Vb. The two largest subfamilies, Clades I and II, contained 237 and 222 PEL members, respectively. The members of Clades Va and Vb only contained four or five motifs, far fewer than the other subfamilies. Gene duplication analysis showed that segmental duplication played a crucial role in the expansion of the PEL gene family in Gossypium species. The PELs from Clades I, IV, Va, and Vb were expressed during the fiber elongation stage, but nearly all PEL genes from Clades II and III showed no expression in any of the investigated fiber developmental stages. We further performed single-gene haplotype association analysis in 2,001 G. hirsutum accessions and 229 G. barbadense accessions. Interestingly, 14 PELs were significantly associated with fiber length and strength traits in G. barbadense with superior fiber quality, while only eight GhPEL genes were found to be significantly associated with fiber quality traits in G. hirsutum. Our findings provide important information for further evolutionary and functional research on the PEL gene family members and their potential use for fiber quality improvement in cotton.

Key words: Malvaceae , pectate lyase (PEL) , Gossypium species , fiber quality

Qian Deng, Zeyu Dong, Zequan Chen, Zhuolin Shi, Ting Zhao, Xueying Guan, Yan Hu, Lei Fang. 锦葵科植物果胶酸裂解酶（PEL）基因家族的全基因组鉴定及其对棉花纤维品质的影响[J]. Journal of Integrative Agriculture, 2024, 23(10): 3264-3282.

Qian Deng, Zeyu Dong, Zequan Chen, Zhuolin Shi, Ting Zhao, Xueying Guan, Yan Hu, Lei Fang. Genome-wide identification of the pectate lyase (PEL) gene family members in Malvaceae, and their contribution to cotton fiber quality[J]. Journal of Integrative Agriculture, 2024, 23(10): 3264-3282.

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