Table_2_High-density linkage to physical mapping in a unique Tall × Dwarf coconut (Cocos nucifera L.) outbred F2 uncovers a major QTL for flowering time colocalized with the FLOWERING LOCUS T (FT).xlsx

IntroductionThe coconut tree crop (Cocos nucifera L.) provides vital resources for millions of people worldwide. Coconut germplasm is largely classified into ‘Tall’ (Typica) and ‘Dwarf’ (Nana) types. While Tall coconuts are outcrossing, stress tolerant, and late flowering, Dwarf coconuts are inbred and flower early with a high rate of bunch emission. Precocity determines the earlier production of a plantation and facilitates management and harvest.
MethodsA unique outbred F2 population was used, generated by intercrossing F1 hybrids between Brazilian Green Dwarf from Jiqui (BGDJ) and West African Tall (WAT) cultivars. Single-nucleotide polymorphism (SNP) markers fixed for alternative alleles in the two varieties, segregating in an F2 configuration, were used to build a high-density linkage map with ~3,000 SNPs, anchored to the existing chromosome-level genome assemblies, and a quantitative trait locus (QTL) mapping analysis was carried out.
ResultsThe linkage map established the chromosome numbering correspondence between the two reference genome versions and the relationship between recombination rate, physical distance, and gene density in the coconut genomes. Leveraging the strong segregation for precocity inherited from the Dwarf cultivar in the F2, a major effect QTL with incomplete dominance was mapped for flowering time. FLOWERING LOCUS T (FT) gene homologs of coconut previously described as putatively involved in flowering time by alternative splice variant analysis were colocalized within a ~200-kb window of the major effect QTL [logarithm of the odds (LOD) = 11.86].
DiscussionOur work provides strong phenotype-based evidence for the role of the FT locus as the putative underlying functional variant for the flowering time difference between Dwarf and Tall coconuts. Major effect QTLs were also detected for developmental traits of the palm, plausibly suggesting pleiotropism of the FT locus for other precocity traits. Haplotypes of the two SNPs flanking the flowering time QTL inherited from the Dwarf parent BGDJ caused a reduction in the time to flower of approximately 400 days. These SNPs could be used for high-throughput marker-assisted selection of early-flowering and higher-productivity recombinant lines, providing innovative genetic material to the coconut industry.

引言
经济椰树（Cocos nucifera L.）为全球数百万民众提供了至关重要的生存资源。椰树种质资源主要可分为高种椰（Tall, Typica）与矮种椰（Dwarf, Nana）两大类型。高种椰为异花授粉、抗逆性强且开花较晚，而矮种椰为自交系、开花早且果穗发生率高。早花性决定了椰园可提前投产，同时便于田间管理与采收作业。
方法
本研究采用了一个独特的异交F2群体，该群体由来自吉基的巴西青矮椰（Brazilian Green Dwarf from Jiqui, BGDJ）与西非高椰（West African Tall, WAT）品种杂交获得的F1代杂种再互交产生。利用在两个品种中固定了不同等位基因、且在F2群体中发生分离的单核苷酸多态性（single-nucleotide polymorphism, SNP）标记，构建了包含约3000个SNP的高密度连锁图谱，该图谱锚定至已有的染色体级基因组组装序列，并开展了数量性状位点（quantitative trait locus, QTL）定位分析。
结果
该连锁图谱明确了两个参考基因组版本间的染色体编号对应关系，以及椰树基因组中重组率、物理距离与基因密度之间的关联。依托F2群体中源自矮种椰的强早花性分离性状，本研究定位到一个具有不完全显性效应的主效QTL，调控开花时间。此前通过可变剪接变体分析被推测参与开花时间调控的椰树FLOWERING LOCUS T（FT）基因同源序列，与该主效QTL的约200kb区间共定位[似然比对数（logarithm of the odds, LOD）值为11.86]。
讨论
本研究为FT位点作为调控矮种与高种椰树开花时间差异的潜在功能性变异位点提供了强有力的表型证据。本研究还检测到调控椰树发育性状的主效QTL，由此推测FT位点对其他早花相关性状可能存在多效性。源自矮本亲本BGDJ的、位于开花时间QTL两侧的两个SNP单体型，可使开花时间缩短约400天。这些SNP标记可用于高通量标记辅助选择早花、高产重组株系，为椰树产业提供创新性的遗传材料。