抗裂和易裂箭筈豌豆种质的裂荚特性差异与木质素生物合成有关

doi:10.1016/j.jia.2024.03.032

摘要/Abstract

摘要：

箭筈豌豆是一种自花授粉的一年生豆科牧草，分布于世界各地。它具有广泛的适应性和高营养价值，常被用作牲畜饲料的重要蛋白质来源。然而，箭筈豌豆的荚果破裂严重限制了其产量。为了阐明箭筈豌豆荚果破裂的机制，我们选择了3个抗裂（SR）种质（B65、B135和B392）和3个易裂（SS）种质（L33、L170和L461）的荚皮进行转录组测序。在盛花期后5、10、15、20和25天的B135和L461箭筈豌豆荚皮中共鉴定到17190个差异表达基因（DEGs）。KEGG分析显示，“苯丙烷生物合成”是最显著富集的通路，并且在B135和L461荚皮中鉴定出40个与木质素生物合成相关的结构基因，并在两者之间差异表达。此外，我们分析了盛花期后15天的3个SR和3个SS箭筈豌豆种质荚皮的DEGs，大部分DEGs的功能与在B135和L461箭筈豌豆不同发育时期中鉴定的富集通路一致。SR种质的总木质素含量显著低于SS种质。本研究为揭示箭筈豌豆裂荚特性与木质素生物合成相关的分子调控机制奠定了基础，并为育种家进一步培育抗裂荚箭筈豌豆提供了可参考的功能基因。

Abstract:

The common vetch (Vicia sativa L.) is a self-pollinated annual forage legume that is widely distributed worldwide. It has wide adaptability and high nutritional value and is commonly used as an important protein source for livestock feed. However, pod shattering seriously limits the yield of common vetch. To clarify the mechanism of pod shattering in common vetch, the pod walls of three shattering-resistant (SR) accessions (B65, B135, and B392) and three shattering-susceptible (SS) accessions (L33, L170, and L461) were selected for transcriptome sequencing. A total of 17,190 differentially expressed genes (DEGs) were identified in the pod wall of B135 and L461 common vetch at 5, 10, 15, 20, and 25 days after anthesis. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that “phenylpropanoid biosynthesis” was the most significantly enriched pathway, and 40 structural genes associated with lignin biosynthesis were identified and differentially expressed in B135 and L461 common vetch. We analysed the DEGs in the pod wall of three SR and three SS accessions at 15 days after anthesis, and most of the DEGs were consistent with the significant enrichment pathways identified in B135 and L461 common vetch. The total lignin content of SR accessions was significantly lower than the SS accessions. The present study lays a foundation for understanding the molecular regulatory mechanism of pod shattering related to lignin biosynthesis in common vetch and provides reference functional genes for breeders to further cultivate shattering-resistant common vetch varieties.

Key words: Vicia sativa L. , pod shattering , pod wall , transcriptome , lignin biosynthesis

Xueming Dong, Jiwei Chen, Qiang Zhou, Dong Luo, Longfa Fang, Wenxian Liu, Zhipeng Liu. 抗裂和易裂箭筈豌豆种质的裂荚特性差异与木质素生物合成有关[J]. Journal of Integrative Agriculture, 2025, 24(12): 4528-4545.

Xueming Dong, Jiwei Chen, Qiang Zhou, Dong Luo, Longfa Fang, Wenxian Liu, Zhipeng Liu. Pod-shattering characteristic differences between shattering-resistant and shattering-susceptible common vetch accessions are associated with lignin biosynthesis[J]. Journal of Integrative Agriculture, 2025, 24(12): 4528-4545.

参考文献

Abd El-Moneim A M. 1993. Selection for non-shattering common vetch, Vicia sativa L. Plant Breeding, 110, 168–171.

Ballester P, Ferrandiz C. 2016. Shattering fruits: Variations on a dehiscent theme. Current Opinion in Plant Biology, 35, 68–75.

Boerjan W, Ralph J, Baucher M. 2003. Lignin biosynthesis. Annual Review of Plant Biology, 54, 519–546.

Bonawitz N D, Chapple C. 2010. The genetics of lignin biosynthesis: Connecting genotype to phenotype. Annual Review of Genetics, 44, 337–363.

Buchfink B, Xie C, Huson D H. 2015. Fast and sensitive protein alignment using diamond. Nature Methods, 12, 59–60.

Christiansen L C, Degan F D, Ulvskov P, Borkhardt B. 2002. Examination of the dehiscence zone in soybean pods and isolation of a dehiscence-related endopolygalacturonase gene. Plant Cell and Environment, 25, 479–490.

Chu W, Liu J, Cheng H T, Li C, Fu L, Wang W X, Wang H, Hao M Y, Mei D D, Liu K D, Hu Q. 2022. A lignified-layer bridge controlled by a single recessive gene is associated with high pod-shatter resistance in Brassica napus L. The Crop Journal, 10, 638–646.

Davies G C, Bruce D M. 1997. Fracture mechanics of oilseed rape pods. Journal of Materials Science, 32, 5895–5899.

Dong D K, Yan L F, Dong R, Liu W X, Wang Y R, Liu Z P. 2017. Evaluation and analysis of pod dehiscence factors in shatter-susceptible and shatter-resistant common vetch. Crop Science, 57, 2770–2776.

Dong R, Dong D K, Luo D, Zhou Q, Chai X T, Zhang J Y, Xie W G, Liu W X, Dong Y, Wang Y R, Liu Z P. 2017. Transcriptome analyses reveal candidate pod shattering-associated genes involved in the pod ventral sutures of common vetch (Vicia sativa L.). Frontiers in Plant Science, 8, 649.

Dong R, Jahufer M Z, Dong D K, Wang Y R, Liu Z P. 2016. Characterization of the morphological variation for seed traits among 537 germplasm accessions of common vetch (Vicia sativa L.) using digital image analysis. New Zealand Journal of Agricultural Research, 59, 422–435.

Dong X C, Qian T F, Chu J P, Zhang X, Liu Y J, Dai X L, He M R. 2023. Late sowing enhances lodging resistance of wheat plants by improving the biosynthesis and accumulation of lignin and cellulose. Journal of Integrative Agriculture, 22, 1351–1365.

Dong Y, Wang Y Z. 2015. Seed shattering: From models to crops. Frontiers in Plant Science, 6, 476.

Dong Y, Yang X, Liu J, Wang B H, Liu B L, Wang Y Z. 2014. Pod shattering resistance associated with domestication is mediated by a NAC gene in soybean. Nature Communications, 5, 3352.

Franke Q, McMichael C M, Meyer K, Shirley A M, Cusumano J C, Chapple C. 2000. Modified lignin in tobacco and poplar over-expressing the Arabidopsis gene encoding ferulate 5-hydroxylase. The Plant Journal, 22, 223–234.

Funatsuki H, Suzuki M, Hirose A, Inaba H, Yamada T, Hajika M, Komatsu K, Katayama T, Sayama T, Ishimoto M, Fujino K. 2014. Molecular basis of a shattering resistance boosting global dissemination of soybean. Proceedings of the National Academy of Sciences of the United States of America, 111, 17797–17802.

Guo M W, Zhu L, Li H Y, Liu W P, Wu Z N, Wang C H, Liu L, Li Z Y, Li J. 2022. Mechanism of pod shattering in the forage legume Medicago ruthenica. Plant Physiology and Biochemistry, 185, 260–267.

Huang Y F, Gao X L, Nan Z B, Zhang Z X. 2017. Potential value of the common vetch (Vicia sativa L.) as an animal feedstuff: A review. Journal of Animal Physiology and Animal Nutrition, 101, 807–823.

Jia C L, Dong D K, Zhou Q, Searle I R, Liu Z P. 2021. Significant cell differences in pod ventral suture in shatter-resistant and shatter-susceptible common vetch accessions. Crop Science, 61, 1749–1759.

Jia J, Wang H, Cai Z D, Wei R Q, Huang J H, Xia Q J, Xiao X H, Ma Q B, Nian H, Cheng Y B. 2022. Identification and validation of stable and novel quantitative trait loci for pod shattering in soybean [Glycinemax (L.) Merr.]. Journal of Integrative Agriculture, 21, 3169–3184.

Jiang L Y, Ma X, Zhao S S, Tang Y Y, Liu F X, Gu P, Fu Y C, Zhu Z F, Cai H W, Sun C Q, Tan L B. 2019. The APETALA2-like transcription factor SUPERNUMERARY BRACT controls rice seed shattering and seed size. The Plant Cell, 31, 17–36.

Kang X, Cai J J, Chen Y X, Yan Y C, Yang S T, He R Q, Wang D, Zhu Y L. 2019. Pod-shattering characteristics differences between two groups of soybeans are associated with specific changes in gene expression. Functional and Integrative Genomics, 20, 201–210.

Kim D, Langmead B, Salzberg S L. 2015. HISAT: A fast spliced aligner with low memory requirements. Nature Methods, 12, 357–360.

Kuai J, Sun Y Y, Guo C, Zhao L, Zuo Q S, Wu J S, Zhou G S. 2017. Root-applied silicon in the early bud stage increases the rapeseed yield and optimizes the mechanical harvesting characteristics. Filed Crops Research, 200, 88–97.

Li C, Zhou A, Sang T. 2006. Rice domestication by reducing shattering. Science, 311, 1936–1939.

Li L F, Olsen K M. 2016. Chapter three-to have and to hold: Selection for seed and fruit retention during crop domestication. Current Topics in Developmental Biology, 119, 63–109.

Liljegren S J, Ditta G S, Eshed Y, Savidge B, Bowman J L, Yanofsky M F. 2000. SHATTERPROOF MADS-box genes control seed dispersal in Arabidopsis. Nature, 404, 766–770.

Liljegren S J, Roeder A H K, Kempin S A, Gremski K, Østergaard L, Guimil S, Reyes D K, Yanofsky M F. 2004. Control of fruit patterning in Arabidopsis by INDEHISCENT. Cell, 116, 843–853.

Livak K J, Schmittgen T D. 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2–ΔΔCT method. Methods, 25, 402–408.

Lo S, Parker T, Muñoz-Amatriaín M, Berny-Mier J C, Teran Y, Jernstedt J, Close T J, Gepts P. 2021. Genetic, anatomical, and environmental patterns related to pod shattering resistance in domesticated cowpea [Vigna unguiculata (L.) Walp]. Journal of Experimental Botany, 72, 6219–6229.

Meyer J, Shirley A M, Cusumano J C, Bell-Lelong D A, Chapple C. 1998. Lignin monomer composition is determined by the expression of a cytochrome P450-dependent monooxygenase in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America, 95, 6619–6623.

Miller A J, Gross B L. 2011. From forest to field: Perennial fruit crop domestication. American Journal of Botany, 98, 1389–1414.

Mitsuda N, Ohme-Takagi M. 2008. NAC transcription factors NST1 and NST3 regulate pod shattering in a partially redundant manner by promoting secondary wall formation after the establishment of tissue identity. The Plant Journal, 56, 768–778.

Murgia M L, Attene G, Rodriguez M, Bitocchi E, Bellucci E, Fois D, Nanni L, Gioia T, Albani D M, Papa R, Rau D. 2017. A comprehensive phenotypic investigation of the ‘pod-shattering syndrome’ in common bean. Frontiers in Plant Science, 8, 251.

Muriira N G, Xu W, Muchugi A, Xu J C, Liu A Z. 2015. De novo sequencing and assembly analysis of transcriptome in the Sodom apple (Calotropis gigantea). BMC Genomics, 16, 23.

Ning J, He W, Wu L H, Chang L Q, Hu M, Fu Y C, Liu F X, Sun H Y, Gu P, Ndjiondjop M N, Sun C Q, Zhu Z F. 2023. The MYB transcription factor Seed Shattering 11 controls seed shattering by repressing lignin synthesis in African rice. Plant Biotechnology Journal, 21, 931–942.

Parker T A, Teran J C B M y, Palkovic A, Jernstedt J, Gepts P. 2020. Pod indehiscence is a domestication and aridity resilience trait in common bean. New Phytologist, 225, 558–570.

Pertea M, Pertea G M, Antonescu C M, Chang T C, Mendell J T, Salzberg S L. 2015. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nature Biotechnology, 33, 290–295.

Philbrook B D, Oplinger E S. 1989. Soybean field losses as influenced by harvest delays. Agronomy Journal, 81, 251–258.

Rau D, Murgia M L, Rodriguez M, Bellucci E, Fois D, Albani D, Nanni L, Gioia T, Santo D, Marcolungo L, Delledonne M, Attene G, Papa R. 2018. Genomic dissection of pod shattering in common bean: Mutations at nonorthologous loci at the basis of convergent phenotypic evolution under domestication of leguminous species. The Plant Journal, 97, 693–714.

Reddy M S S, Chen F, Shadle G, Jackson L, Aljoe H, Dixon R A. 2005. Targeted down-regulation of cytochrome P450 enzymes for forage quality improvement in alfalfa (Medicago sativa L.). Proceedings of the National Academy of Sciences of the United States of America, 102, 16573–16578.

Repkova J, Hofbauer J. 2009. Seed pod shattering in the genus Lotus and its overcoming. Czech Journal of Genetics and Plant Breeding, 45, 39–44.

Rippert P, Puyaubert J, Grisollet D, Derrier L, Matringe M. 2009. Tyrosine and phenylalanine are synthesized within the plastids in Arabidopsis. Plant Physiology, 149, 1251–1260.

Rodríguez-Gacio M C, Nicolás C, Matilla A J. 2004. Cloning and analysis of a cDNA encoding an endo-polygalacturonase expressed during the desiccation period of the silique-valves of turnip-tops (Brassica rapa L. cv. Rapa). Journal of Plant Physiology, 161, 219–227.

Seo J H, Kang B K, Dhungana S K, Oh J H, Choi M S, Park J H, Shin S O, Kim H S, Baek I Y, Sung J S, Jung C S, Kim K S, Jun T H. 2020. QTL mapping and candidate gene analysis for pod shattering tolerance in soybean (Glycine max). Plants, 9, 1163.

Suanum W, Somta P, Kongjaimun A, Yimram T, Kaga A, Tomooka N, Takahashi Y, Srinives P. 2016. Co-localization of QTLs for pod fiber content and pod shattering in F2 and backcross populations between yardlong bean and wild cowpea. Molecular Breeding, 36, 1–11.

Tao Z S, Huang Y, Zhang L D, Wang X F, Liu G H, Wang H Z. 2017. BnLATE, a Cys2/His2-type zinc-finger protein, enhances silique shattering resistance by negatively regulating lignin accumulation in the silique walls of Brassica napus. PLoS ONE, 12, e0168046.

Wang Y, Chantreau M, Sibout R, Hawkins S. 2013. Plant cell wall lignification and monolignol metabolism. Frontiers in Plant Science, 4, 220.

Watcharatpong P, Kaga A, Chen X, Somta P. 2020. Narrowing down a major QTL region conferring pod fiber contents in Yardlong Bean (Vigna unguiculata), a vegetable cowpea. Genes, 11, 363.

Xi H W, Nguyen V, Ward C, Liu Z P, Searle I R. 2022. Chromosome-level assembly of the common vetch (Vicia sativa) reference genome. Gigabyte, 2022, 1–19.

Yamada T, Funatsuki H, Hagihara S, Fujita S, Tanaka Y, Tsuji H. 2009. A major QTL, qPDH1, is commonly involved in shattering resistance of soybean cultivars. Breeding Science, 59, 435–440.

Yang C Y, Song J, Ferguson A C, Klisch D, Simpson K, Mo R, Taylor B, Mitsuda N, Wilson Z A. 2017. Transcription factor MYB26 is key to spatial specificity in anther secondary thickening formation. Plant Physiology, 175, 333–350.

Yang J H, Wang H Z. 2016. Molecular mechanisms for vascular development and secondary cell wall formation. Frontiers in Plant Science, 7, 356.

Yoon J, Cho L H, Antt H W, Koh H J, An G. 2017. KNOX protein OSH15 induces grain shattering by repressing lignin biosynthesis genes. Plant Physiology, 174, 312–325.

Zaman Q U, Chu W, Shi Y Q, Hao M Y, Mei D S, Batley J, Zhang B H, Li C, Hu Q. 2021. Characterization of SHATTERPROOF homoeologs and CRISPR-Cas9-mediated genome editing enhances pod-shattering resistance in Brassica napus L. CRISPR Journal, 4, 360–370.

Zhang J P, Singh A K. 2020. Genetic control and geo-climate adaptation of pod dehiscence provide novel insights into soybean domestication. G3 - Genes Genomes Genetics, 10, 545–554.

Zhang Q, Wang L H, Wang Z T, Zhang R T, Liu P, Liu M J, Liu Z G, Zhao Z H, Wang L L, Chen X, Xu H F. 2021. The regulation of cell wall lignification and lignin biosynthesis during pigmentation of winter jujube. Horticulture Research, 8, 238.

Zhang Y, Shen Y Y, Wu X M, Wang J B. 2016. The basis of pod dehiscence: Anatomical traits of the dehiscence zone and expression of eight pod shatter-related genes in four species of Brassicaceae. Biologia Plantarum, 60, 343–354.

Zhao Q. 2016. Lignification: Flexibility, biosynthesis and regulation. Trends in Plant Science, 21, 713–721.

Zhou Y, Lu D F, Li C Y, Luo J H, Zhu B F, Zhu J J, Shangguan Y Y, Wang Z X, Sang T, Zhou B, Han B. 2012. Genetic control of seed shattering in rice by the APETALA2 transcription factor shattering abortion1. The Plant Cell, 24, 1034–1048.