Identification of SBE Gene Family and Development of Functional Markers for TaSBE1-7B in Wheat (Triticum aestivum)
LI Kang-Chun1,2, MA Xu-Guang2, GUO Li-Jian1, TIAN Tian1,3, ZHANG Xian-Feng1,2, WANG Qiao-Yun1,2, YANG De-Long1,2,3,*
1 State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; 2 College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; 3 College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
Abstract：Starch branching enzyme (SBE) is a type of glycosyltransferases that has 2 catalytic functions, it synthesizes and converts amylopectin as part of the starch synthesis pathway. It plays a key regulatory role during grain development in wheat (Triticum aestivum). To investigate the expression characteristics of TaSBE family genes during wheat grain development and identify superior haplotypes, bioinformatics methods were used to identify TaSBE family members across the genome, analyze their expression patterns, and develop and validate functional molecular markers. The results showed that 15 TaSBE genes were found throughout the wheat genome, dispersed on chromosomes 2A, 2B, 2D, 7A, 7B, and 7D. These genes could be divided into 3 subfamilies, with members of the same subfamily sharing comparable gene structures and shared motifs. Intraspecific synteny analysis revealed 9 pairs of chromosomes with intragroup synteny, demonstrating the evolutionary conservation of family members. Analysis of cis-acting elements revealed that TaSBE family genes contain a large number of developmental response elements. RNA-seq and qPCR analysis revealed that the TaSBE1-7A, TaSBE1-7B, and TaSBE1-7D genes were highly expressed in grains. Sequence polymorphism analysis revealed the presence of regular SNP sites in the sequences of TaSBE1-7A and TaSBE1-7B, allowing them to be classified into 2 haplotypes. KASP molecular markers were created for TaSBE1-7A and TaSBE1-7B. The results demonstrated that the KASP marker, positioned at 1 088 bp (G/A) in the TaSBE1-7B complete genome sequence, efficiently discriminated the 2 haplotypes. Associative analysis of grain starch content revealed that varieties with the TaSBE1-7B-HapⅠ haplotype had considerably higher grain starch content than those with TaSBE1-7B-HapⅡ, and TaSBE1-7B-HapⅠ was under positive selection during wheat breeding. This study provides a theoretical foundation for further investigation into the molecular processes by which the TaSBE1 gene controls grain growth and starch synthesis.
李康春, 马旭光, 郭利建, 田甜, 张献丰, 王巧芸, 杨德龙. 小麦淀粉分支酶SBE基因家族鉴定及TaSBE1-7B功能标记开发[J]. 农业生物技术学报, 2026, 34(5): 971-983.
LI Kang-Chun, MA Xu-Guang, GUO Li-Jian, TIAN Tian, ZHANG Xian-Feng, WANG Qiao-Yun, YANG De-Long. Identification of SBE Gene Family and Development of Functional Markers for TaSBE1-7B in Wheat (Triticum aestivum). 农业生物技术学报, 2026, 34(5): 971-983.
[1] 冯政凯, 杨晓莹, 徐晓敏, 等. 2025. 野生二粒小麦SBE基因家族鉴定及表达分析[J]. 麦类作物学报, 45(7): 913-921. (Feng Z K, Yang X Y, Xu X M, et al.2025. Identification and expression analysis of SBE gene family in wild emmer wheat[J]. Journal of Triticeae Crops, 45(7): 913-921.) [2] 傅向东, 刘倩, 李振声, 等. 2018. 小麦基因组研究现状与展望[J]. 中国科学院院刊, 33(9): 909-914. (Fu X D, Liu Q, Li Z S, et al.2018. Research achievement and prospect development on wheat genome[J]. Bulletin of the Chinese Academy of Sciences, 33(9): 909-914.) [3] 赵若男, 邹瑞, Yamamoto Naoki, 等.2024. 小麦WUS基因亚家族的全基因组鉴定及其在雄蕊和雌蕊中的表达分析[J]. 农业生物技术学报, 32(11): 2462-2473. (Zao R N, Zou R, Naoki Y, et al.2024. Genome-wide identification and expression analysis of WUS gene subfamily in wheat pistil and stamen[J]. Journal of Agricultural Biotechnology, 32(11): 2462-2473.) [4] Adegbaju M S, Gouws N, van der Vyver C, et al.2025. Simultaneous repression of GLUCAN WATER DIKINASE 1 and STARCH BRANCHING ENZYME 1 in potato tubers leads to starch with increased amylose and novel industrial properties[J]. Biotechnology Journal, 20(6): e70051. [5] Baguma Y, Sun C X, Ahlandsberg S, et al.2003. Expression patterns of the gene encoding starch branching enzyme Ⅱ in the storage roots of cassava (Manihot esculenta Crantz)[J]. Plant Science, 164(5): 833-839. [6] Baysal C, He W, Drapal M, et al.2020. Inactivation of rice starch branching enzyme Ⅱb triggers broad and unexpected changes in metabolism by transcriptional reprogramming[J]. Proceedings of the National Academy of Sciences of the USA, 117(42): 26503-26512. [7] Blauth S L, Kim K N, Klucinec J, et al.2002. Identification of mutator insertional mutants of starch-branching enzyme 1 (sbe1) in Zea mays L.[J]. Plant Molecular Biology, 48(3): 287-297. [8] Bourne E J, Macey A, Peat S.1945. The enzymic synthesis and degradation of starch. Part Ⅱ. The amylolytic function of the Q-enzyme of the potato[J]. Journal of the Chemical Society (Resumed): 882-888. [9] Cao Y N, Hu W G, Wang C S.2012. Expression profiles of genes involved in starch synthesis in non-waxy and waxy wheat[J]. Russian Journal of Plant Physiology, 59(5): 632-639. [10] Chen C J, Wu Y, Li J W, et al.2023. TBtools-II: A "one for all, all for one" bioinformatics platform for biological big-data mining[J]. Molecular Plant, 16(11): 1733-1742. [11] Collard B C Y, Mackill D J.2008. Marker-assisted selection: an approach for precision plant breeding in the twenty-first century[J]. Philosophical Transactions of the Royal Society B: Biological Sciences, 363(1491): 557-572. [12] Dong M Y, Fan X W, Li Y Z.2019. Cassava AGPase genes and their encoded proteins are different from those of other plants[J]. Planta, 250(5): 1621-1635. [13] Dumez S, Wattebled F, Dauvillee D, et al.2006. Mutants of Arabidopsis lacking starch branching enzyme Ⅱ substitute plastidial starch synthesis by cytoplasmic maltose accumulation[J]. The Plant Cell, 18(10): 2694-2709. [14] Feng L, Fawaz R, Hovde S, et al.2015. Crystal structures of Escherichia coli branching enzyme in complex with linear oligosaccharides[J]. Biochemistry, 54(40): 6207-6218. [15] Fisher D K, Gao M, Kim K N, et al.1996. Two closely related cDNAs encoding starch branching enzyme from Arabidopsis thaliana[J]. Plant Molecular Biology, 30(1): 97-108. [16] Gao M, Fisher D K, Kim K N, et al.1996. Evolutionary conservation and expression patterns of maize starch branching enzyme Ⅰ and Ⅱb genes suggests isoform specialization[J]. Plant Molecular Biology, 30(6): 1223-1232. [17] Guan H, Preiss J.1993. Differentiation of the properties of the branching isozymes from maize (Zea mays)[J]. Plant Physiology, 102(4): 1269-1273. [18] Han Y, Sun F J, Rosales-Mendoza S, et al.2007. Three orthologs in rice, Arabidopsis, and Populus encoding starch branching enzymes (SBEs) are different from other SBE gene families in plants[J]. Gene, 401(1-2): 123-130. [19] He J J, Li C Z, Hu N, et al.2022. ECERIFERUM1-6A is required for the synthesis of cuticular wax alkanes and promotes drought tolerance in wheat[J]. Plant Physiology, 190(3): 1640-1657. [20] Li J Y, Jiao G A, Sun Y W, et al.2021. Modification of starch composition, structure and properties through editing of TaSBEⅡa in both winter and spring wheat varieties by CRISPR/Cas9[J]. Plant Biotechnology Journal, 19(5): 937-951. [21] Liu H X, Si X M, Wang Z Y, et al.2023. TaTPP-7A positively feedback regulates grain filling and wheat grain yield through T6P‐SnRK1 signalling pathway and sugar-ABA interaction[J]. Plant Biotechnology Journal, 21(6): 1159-1175. [22] Livak K J, Schmittgen T D.2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2-ΔΔCT Method[J]. Methods, 25(4): 402-408. [23] Luo S, Ma Q X, Zhong Y Y, et al.2022. Editing of the starch branching enzyme gene SBE2 generates high-amylose storage roots in cassava[J]. Plant Molecular Biology, 108(4): 429-442. [24] Ma L, Li T, Hao C Y, et al.2016. TaGS5-3A, a grain size gene selected during wheat improvement for larger kernel and yield[J]. Plant Biotechnology Journal, 14(5): 1269-1280. [25] Morell M K, Blennow A, Hashemi B K, et al.1997. Differential expression and porperties of starchbranching enzyme isoforms in developing wheat endosperm[J]. Plant Physiology, 113:201-208. [26] Nakamura Y.2002. Towards a better understanding of the metabolic system for amylopectin biosynthesis in plants: Rice endosperm as a model tissue[J]. Plant and Cell Physiology, 43(7): 718-725. [27] Nakamura Y, Takeichi T, Kawaguchi K, et al.1992. Purificationof two forms of starch branching enzyme (Q-enzyme) from developing rice endosperm[J].Physiologia Plantarum, 84(3): 329-335. [28] Nishi A, Nakamura Y, Tanaka N, et al.2001. Biochemical and genetic analysis of the effects of amylose-extender mutation in rice endosperm[J]. Plant Physiology, 127(2): 459-472. [29] Rafalski A.2002. Applications of single nucleotide polymorphisms in crop genetics[J]. Current Opinion in Plant Biology, 5(2): 94-100. [30] Rahman S, Li Z, Abrahams SL, et al.1997. A complex arrangement of genes at a SBEⅠ loucs in wheat[J]. Genome, 40: 465-474. [31] Regina A, Bird A, Top D, et al.2006. High-amylose wheat generated by RNA interference improves indices of large-bowel health in rats[J]. Proceedings of the National Academy of Sciences of the USA, 103(10): 3546-3551. [32] Regina A, Kosar-Hashemi B, Ling S, et al.2010. Control of starch branching in barley defined through differential RNAi suppression of starch branching enzyme Ⅱa and Ⅱb[J]. Journal of Experimental Botany, 61(5): 1469-1482. [33] Repellin A, Baga M, Chibbar RN.2001. Characterization of a cDNA encoding a type Ⅰ starch branchingenzyme produced in developing wheat (Triticum aestivum L.) kernel[J]. Journal of PlantPhysiology, 158(1): 91-100. [34] Rydberg U, Andersson L, Andersson R, et al.2001. Comparison of starch branching enzyme Ⅰ and Ⅱ from potato[J]. European Journal of Biochemistry, 268(23): 6140-6145. [35] Satoh H, Nishi A, Yamashita K, et al.2003. Starch-branching enzyme Ⅰ-deficient mutation specifically affects the structure and properties of starch in rice endosperm[J]. Plant Physiology, 133(3): 1111-1121. [36] Schönhofen A, Zhang X Q, Dubcovsky J.2017. Combined mutations in five wheat STARCH BRANCHING ENZYME Ⅱ genes improve resistant starch but affect grain yield and bread-making quality[J]. Journal of Cereal Science, 75: 165-174. [37] Shimada T, Otani M, Hamada T, et al.2006. Increase of amylose content of sweet potato starch by RNA interference of the starch branching enzyme Ⅱ gene (IbSBEⅡ)[J]. Plant Biotechnology, 23(1): 85-90. [38] Song H Y, Sun H, Dong G Q, et al.2024. NnSBE1 encodes a starch branching enzyme involved in starch biosynthesis in lotus seeds[J]. International Journal of Biological Macromolecules, 279(1): 135104. [39] Sun C X, Sathish P, Ahlandsberg S, et al.1997. Identification of four starch branching enzymes in barley endosperm: partial purification of forms Ⅰ, Ⅱa and Ⅱb[J]. New Phytologist, 137(2): 215-222. [40] Sun C X, Sathish P, Ek B, et al.1996. Demonstration of in vitro starch branching enzyme activity for a 51/50-kDa polypeptide isolated from developing barley (Hordeum vulgare) caryopses[J]. Physiologia Plantarum, 96(3): 473-483. [41] Sun Y W, Jiao G A, Liu Z P, et al.2017. Generation of high-amylose rice through CRISPR/Cas9-mediated targeted mutagenesis of starch branching enzymes[J]. Frontiers in Plant Science, 8: 298. [42] Tadesse W, Sanchez-Garcia M, Assefa S G, et al.2019. Genetic gains in wheat breeding and its role in feeding the world[J]. Crop Breeding, Genetics and Genomics, 1(1): e190005. [43] Takeda Y, Guan H P, Preiss J.1993. Branching of amylose by the branching isoenzymes of maize endosperm[J]. Carbohydrate Research, 240: 253-263. [44] Takeuchi A, Ohnuma M, Teramura H, et al.2021. Creation of a potato mutant lacking the starch branching enzyme gene StSBE3 that was generated by genome editing using the CRISPR/dMac3-Cas9 system[J]. Plant Biotechnology, 38(3): 345-353. [45] Tetlow I J, Emes M J.2014. A review of starch‐branching enzymes and their role in amylopectin biosynthesis[J]. IUBMB life, 66(8): 546-558. [46] Tuncel A, Corbin K R, Ahn-Jarvis J, et al.2019. Cas9-mediated mutagenesis of potato starch-branching enzymes generates a range of tuber starch phenotypes[J]. Plant Biotechnology Journal, 17(12): 2259-2271. [47] Ullah R, Yin M Y, Li S.2024. Genome-wide association study identifies loci and candidate genes for RVA parameters in wheat (Triticum aestivum L.)[J].Frontiers in Plant Science, 15: 1421924. [48] Wang W X, Wang Z H, Li X T, et al.2020. SnpHub: An easy-to-set-up web server framework for exploring large-scale genomic variation data in the post-genomic era with applications in wheat[J]. GigaScience, 9(6): giaa060. [49] Wu L F, Xie Z C, Li D P, et al.2024. TaMYB72 directly activates the expression of TaFT to promote heading and enhance grain yield traits in wheat (Triticum aestivum L.)[J]. Journal of Integrative Plant Biology, 66(7): 1266-1269. [50] Yandeau-Nelson M D, Laurens L, Shi Z, et al.2011. Starch-branching enzyme Ⅱa is required for proper diurnal cycling of starch in leaves of maize[J]. Plant Physiology, 156(2): 479-490. [51] Yu J W, Wang K Y, Beckles D M.2021. Starch branching enzymes as putative determinants of postharvest quality in horticultural crops[J]. BMC Plant Biology, 21(1): 1-16. [52] Zhang L, Sun W T, Gao W D, et al.2024. Genome-wide identification and analysis of the GGCT gene family in wheat[J]. BMC Genomics, 25(1): 1-14. [53] Zhao Y J, Li N, Li B, et al.2015. Reduced expression of starch branching enzyme Ⅱa and Ⅱb in maize endosperm by RNAi constructs greatly increases the amylose content in kernel with nearly normal morphology[J]. Planta, 241(2): 449-461.
