Fang Xiaojian, Liu Hangqin, Liu Jiacheng, Song Yang, Xu Min, Jian Xing, Dong Li, Zhang Qianwen, Xu Le, Fan Guorui, Wang Zhaoying, You Yiwen, Feng Tianyu, Li Wenyu, Li Yuling, Song Rentao, Lin Zhongwei
State Key Laboratory of Maize Bio-Breeding, National Maize Improvement Center, Department of Crop Genetics and Breeding, China Agricultural University, Beijing, China.
Sanya Institute of China Agricultural University, Sanya, Hainan, China.
Plant Biotechnol J. 2025 Jul;23(7):2911-2927. doi: 10.1111/pbi.70125. Epub 2025 May 5.
Popcorn, one of the world's most popular snack foods, represents the most ancient type of maize domesticated by humans. However, the genetic basis underlying popcorn evolution and kernel-popping traits remains largely unknown. In this study, we assembled a high-quality genome sequence of the popcorn landrace Strawberry Popcorn (SP) and conducted extensive population genomic analyses. The SP genome spans 2.3 Gb and harbours a large inversion on chromosome 8, along with millions of genetic variants that enable the discovery of beneficial alleles. Translocations and substantial duplications of the Ga1 gene occurred in the locus associated with unilateral cross-incompatibility on chromosome 4. Tandemly duplicated Ga1 genes underwent pseudogenisation and truncation with complete loss of gene function. The P1 gene experienced gene expansion and regulatory modifications, leading to downregulation of transcription and subsequent loss of pericarp colour during maize domestication and improvement. Population genomic analysis further identified a subset of 12 marker genes from over 2494 genes under human selection, which were reshaped to enhance kernel-popping traits during domestication. These marker genes include Pl1 and Dek1 for pericarp and aleurone layer thickness; THP9, Sh2, SUS1, Smk10, KW1, O7, and NKD1 for protein and starch biosynthesis; and VP5, CCD7, and Crti3 for carotene biosynthesis, which all influence endosperm vitreousness, a key factor determining kernel hardness for popping. Among these genes, KW1 and O7 stand out as pivotal genes with a significant impact on kernel-popping performance. These results provide a wealth of gene targets to greatly accelerate the molecular breeding of improved popcorn varieties.
爆米花是全球最受欢迎的休闲食品之一，代表了人类驯化的最古老的玉米类型。然而，爆米花进化和爆粒特性背后的遗传基础在很大程度上仍然未知。在本研究中，我们组装了爆米花地方品种草莓爆米花（SP）的高质量基因组序列，并进行了广泛的群体基因组分析。SP基因组跨度为2.3Gb，在8号染色体上存在一个大的倒位，以及数百万个遗传变异，这些变异有助于发现有益等位基因。在4号染色体上与单侧杂交不亲和相关的位点发生了Ga1基因的易位和大量重复。串联重复的Ga1基因经历了假基因化和截短，导致基因功能完全丧失。P1基因经历了基因扩增和调控修饰，导致在玉米驯化和改良过程中转录下调以及随后果皮颜色丧失。群体基因组分析进一步从超过2494个受人类选择的基因中鉴定出12个标记基因子集，这些基因在驯化过程中经过重塑以增强爆粒特性。这些标记基因包括用于果皮和糊粉层厚度的Pl1和Dek1；用于蛋白质和淀粉生物合成的THP9、Sh2、SUS1、Smk10、KW1、O7和NKD1；以及用于类胡萝卜素生物合成的VP5、CCD7和Crti3，它们都影响胚乳透明度，这是决定爆粒时籽粒硬度的关键因素。在这些基因中，KW1和O7作为对爆粒性能有重大影响的关键基因脱颖而出。这些结果提供了丰富的基因靶点，可极大地加速改良爆米花品种的分子育种。
