Map-based Cloning and Functional Characterization of AGL1, a Gene Regulating Lemma and Palea Development in Rice

doi:10.16819/j.1001-7216.2026.250909

Abstract

Abstract: 【Objective】Rice lemma and palea development directly affects grain shape, pollination efficiency, yield and quality. This study identified mutants related to rice glume development, mapped and cloned the causal genes, and elucidated the molecular mechanisms by which the target genes regulate glume development, providing theoretical references for rice molecular breeding. 【Methods】The agl1 mutant was obtained by EMS mutagenesis of japonica cultivar SN9816. Paraffin sectioning and scanning electron microscopy were used to observe the morphology of glumes and floral organs; pollen viability was assessed by I₂-KI staining. Map-based cloning delimited AGL1, candidate genes were sequenced, and conservation and diversity of the target gene were analyzed. A Foss grain analyzer was used to measure brown-rice quality parameters.【Results】Compared with the wild-type SN9816, agl1 showed more strongly curved lemmas with unchanged longitudinal length, inwardly sunken paleae, and significantly narrowed lemma and palea; the lemma almost completely enclosed the palea. agl1 displayed abnormal lodicules, enlarged pistils and disordered stamens. Pollen activity and seed-setting rate were reduced. AGL1 was fine-mapped to a 68.7-kb interval between Indel4 and Indel5 on chromosome 2. Sequencing seven ORFs in this region revealed a single-nucleotide mutation in LOC_Os02g56610, which encodes a DUF640-domain protein. The DUF640 family in rice harbors a conserved ALOG domain and diverse regulatory elements, suggesting roles in both floral morphogenesis and grain quality. Quality analysis showed increased brown-rice protein and free fatty acid content but decreased amylose and total starch content, leading to poorer eating quality. 【Conclusion】The AGL1 gene functions as a pivotal regulator of rice lemma and palea development and grain quality; its loss-of-function disrupts hull morphogenesis, compromises pollen viability, and likely perturbs the grain-filling process, resulting in the concomitant deterioration of both yield and grain quality.

Key words: aberrant rice lemma, grain shape, pollen viability, map-based cloning, eating quality, DUF640 family

摘要： 【目的】水稻颖壳发育直接影响籽粒形态、授粉效率、产量与品质。本研究通过鉴定水稻颖壳发育相关突变体，对突变性状基因进行定位克隆，阐明目标基因调控颖壳发育的分子调控机理，可为水稻分子育种提供理论参考。【方法】利用EMS诱变粳稻品种SN9816获得agl1突变体。通过石蜡切片、扫描电镜观察颖壳及花器官形态结构，碘-碘化钾染色法测定花粉活力。利用图位克隆技术对AGL1进行定位，对候选基因测序，同时分析目标基因的保守性和多样性。采用Foss谷物分析仪测定糙米品质参数。【结果】与野生型SN9816相比，突变体agl1的外稃弯曲程度更大，纵向长度没有变化，内稃向内凹陷，内、外稃宽度明显缩小，外稃极大程度包裹住内稃。突变体agl1的浆片形态异常，雌蕊增大，雄蕊排列紊乱；通过测定花粉活性发现，agl1的花粉活性降低，导致结实率下降。利用图位克隆的方法将AGL1定位在2号染色体标记Indel4与Indel5之间，物理距离为68.7 kb。对区间内的7个ORF (open reading frames)测序，发现LOC_Os02g56610在突变体中发生一个单碱基突变，该基因编码一个DUF640结构域蛋白。DUF640家族在水稻中具有保守的ALOG结构域和多样的表达调控元件，其突变可能不仅调控花器官形态建成，在稻米品质中还具有重要作用。米质测定结果表明，糙米蛋白质与游离脂肪酸含量升高，直链淀粉与总淀粉含量降低，导致食味品质下降。【结论】AGL1 基因是调控水稻颖壳发育和米质的关键因子，其功能缺失影响了稃壳形态建成，降低花粉活力，并可能干扰了籽粒灌浆过程，导致产量与品质双双劣变。

关键词: 水稻畸形颖壳, 籽粒形态, 花粉活性, 图位克隆, 食味品质, DUF640家族

FENG Pulin, YANG Qiwen, WU Jiayi, FAN Mingqian, CHENG Yanshuang, QIU Zhonghua, GUO Ran, CHEN Wenfu, WANG Jiayu. Map-based Cloning and Functional Characterization of AGL1, a Gene Regulating Lemma and Palea Development in Rice[J]. Chinese Journal OF Rice Science, 2026, 40(5): 607-617.

冯莆淋, 杨绮文, 吴佳益, 范鸣谦, 程艳双, 邱忠华, 郭然, 陈温福, 王嘉宇. 水稻颖壳发育基因AGL1的图位克隆与功能分析[J]. 中国水稻科学, 2026, 40(5): 607-617.

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