基于侗族传统文化的香禾糯起源演化研究

“Kam Sweet Rice” (KSR) is an special kind of original ecological rice landrace and has been cultivated for thousands of years in southeast of Guizhou province, It has many special qualities, including strong aromatic flavor, well glutinous features, difficulty of threshing, and strong resistance to adverse situation. Plentiful KSR resources are the indispensable materials basis and cultural symbol in the production and daily life and culture customs of Dong people. In recent years, although KSR have reduced in large area and variety quantities, which are still cultivated influenced by Dong’s traditional culture. From the result of our previous study, KSR resources had an origin and genetic evolution relationship with other rice landraces or wild rice germplasms from Guizhou and other provinces, but only focus on the specific gene, not the whole-genome level. In addition, the cultivator and breeder of KSR---Dong people, is a migration group from the adjacent provinces to Qiandongnan area, which may have a closely connection with the domestication of KSR. In view of this, we selected typical materials with broad resources and high genetic diversity, including KSR varieties, other rice landraces from Guizhou province, rice landraces from other adjacent provinces, and some wild rice varieties. Taking the whole-genome sequencing methods, we will perform the first analysis of origin and evolution of Kam Sweet Rice based on Dong’s traditional culture. Through the analysis of nucleotide variation, population structure, selection sweep, phylogenetic and geographic analyses, and the type and frequency variation of SNP related KSR traits, we will study the genetic variation and selection printing, explore the process of origin and evolution of KSR based on Dong’s migration route and traditional culture. The main agronomic characters and quality traits including fragrance, glutinous, falling grain and awn will be investigated, and then identify excellent alleles and functional haplotypes with the methods of genome-wide association study (GWAS). This study is of great significance to reasonably protect and utilize KSR, create excellent germplasm resources and promote ethnic traditional knowledge.

香禾糯是黔东南千百年种植的一类特殊原始生态型稻种，具有香味浓、糯性强、难脱粒、抗逆强等特性，是我国重要的水稻基因资源，受侗族文化影响至今仍持续种植。然而，香禾糯的起源演化和基因定位尚缺乏系统研究。我们前期发现其特定基因序列与贵州及周边省份的栽培稻和野生稻具有遗传相似性，但没覆盖全基因组水平。而且，香禾糯的起源演化可能与侗族迁徙和民族传统文化相关。鉴于此，本研究选取典型的香禾糯稻种、贵州其他稻种、周边省份栽培稻及野生稻为试验材料，采用全基因组重测序技术，开展基于侗族传统文化的香禾糯起源演化研究。通过遗传多样性、群体结构、选择消除、亲缘地理学，以及品质特性相关基因的单倍型变化分析，揭示香禾糯与其他稻种的遗传变异，阐明香禾糯起源演化过程。并对主要农艺性状及香味、糯性、落粒性、芒性等进行鉴定，采用全基因组关联分析，挖掘优异等位变异和功能单倍型。本研究对充分利用香禾糯及保护侗族传统文化具有重要意义。

香禾糯是贵州省黔东南州的一类特殊地方稻种资源，受侗族传统文化影响被持续种植利用上千年，具有香味浓、糯性强、耐寒冷及抗病虫等特性，因此开展香禾糯资源的保护利用及优异基因发掘对水稻育种具有重要意义。然而，香禾糯的起源演化和基因定位尚缺乏系统研究。我们前期发现其特定基因序列与贵州及周边省份的栽培稻和野生稻具有遗传相似性，但没覆盖全基因组水平。而且，香禾糯的起源演化可能与侗族迁徙和民族传统文化相关。鉴于此，本研究选取104份香禾糯资源、104份贵州其他地方稻种及164份周边省份地方稻种为试验材料，基于主要农艺性状与全基因组高通量测序分析，阐明侗族传统文化背景下香禾糯的遗传演化规律，挖掘优异基因和功能单倍型，对充分利用香禾糯及保护侗族传统文化具有重要意义。系统发育和农艺性状表型分析发现，香禾糯与福建、广东、广西及江西省地方稻种存在遗传演化关系；基因流计算发现，以上四省的地方稻种对香禾糯的基因渗入与其他地区相比具有显著差异，是香禾糯的直接供体，说明香禾糯是由这些省份的地方稻种演化而来，该演化规律与侗族族源及迁徙路线一致。通过SMC++分析发现，侗族先民对香禾糯的驯化大约在350年前完成，使香禾糯形成独特的群体特征并世代相传至今，但其有效种群规模呈锐减趋势，香禾糯优异种质资源亟需保护。选择消除分析发现香禾糯在被侗族千百年来的驯化过程中，其群体中的DPS1基因、Hd1基因和GS3基因分别在增加结实率、改变抽穗期和改变籽粒大小等方面被选择，与祖先群体相比香禾糯的籽粒更圆润饱满、千粒重增加。耐冷性调控基因LTG1及MYBS3被选择，这些变异均符合香禾糯的遗传演化规律，体现了驯化过程中侗族发挥的积极作用。全基因组关联分析（GWAS）的8个农艺性状及1个耐冷性状中共定位到103个显著位点，发现Os02g0202900和Os09g0471100以及Os01g0923300基因在千粒重和穗粒数调控方面贡献显著；其中，Os01g0923300基因的单倍型Hap1在香禾糯群体中表现特殊，是侗族对香禾糯驯化过程中产生的一个特殊优势单倍型。