Table_3.XLSX

Using interspecific crosses involving Oryza glaberrima Steud. as donor and O. sativa L. as recurrent parents, rice breeders at the Africa Rice Center developed several ‘New Rice for Africa (NERICA)’ improved varieties. A smaller number of interspecific and intraspecific varieties have also been released as ‘Advanced Rice for Africa (ARICA)’. The objective of the present study was to investigate the genetic variation, relatedness, and population structure of 330 widely used rice genotypes in Africa using DArTseq-based single nucleotide polymorphisms (SNPs). A sample of 11 ARICAs, 85 NERICAs, 62 O. sativa spp. japonica, and 172 O. sativa spp. indica genotypes were genotyped with 27,560 SNPs using diversity array technology (DArT)-based sequencing (DArTseq) platform. Nearly 66% of the SNPs were polymorphic, of which 15,020 SNPs were mapped to the 12 rice chromosomes. Genetic distance between pairs of genotypes that belong to indica, japonica, ARICA, and NERICA varied from 0.016 to 0.623, from 0.020 to 0.692, from 0.075 to 0.763, and from 0.014 to 0.644, respectively. The proportion of pairs of genotypes with genetic distance > 0.400 was the largest within NERICAs (35.1% of the pairs) followed by ARICAs (18.2%), japonica (17.4%), and indica (5.6%). We found one pair of japonica, 11 pairs of indica, and 35 pairs of NERICA genotypes differing by <2% of the total scored alleles, which was due to 26 pairs of genotypes with identical pedigrees. Cluster analysis, principal component analysis, and the model-based population structure analysis all revealed two distinct groups corresponding to the lowland (primarily indica and lowland NERICAs) and upland (japonica and upland NERICAs) growing ecologies. Most of the interspecific lowland NERICAs formed a sub-group, likely caused by differences in the O. glaberrima genome as compared with the indica genotypes. Analysis of molecular variance revealed very great genetic differentiation (FST = 0.688) between the lowland and upland ecologies, and 31.2% of variation attributable to differences within cluster groups. About 8% (1,197 of 15,020) of the 15,020 SNPs were significantly (P < 0.05) different between the lowland and upland ecologies and formed contrasting haplotypes that could clearly discriminate lowland from upland genotypes. This is the first study using high density markers that characterized NERICA and ARICA varieties in comparison with indica and japonica varieties widely used in Africa, which could aid rice breeders on parent selection for developing new improved rice germplasm.非洲水稻中心的水稻育种团队以光稃稻（Oryza glaberrima Steud.）为供体亲本、栽培稻（Oryza sativa L.）为轮回亲本开展种间杂交，成功培育出多个“非洲新稻（New Rice for Africa, NERICA）”改良品种。另有少量种间及种内品种被审定为“非洲先进稻（Advanced Rice for Africa, ARICA）”并推广应用。本研究旨在利用基于多样性阵列技术测序（DArTseq）的单核苷酸多态性（SNPs）标记，解析非洲地区广泛应用的330份水稻基因型的遗传变异、亲缘关系及群体结构。试验共纳入11份ARICA、85份NERICA、62份粳稻（O. sativa spp. japonica）及172份籼稻（O. sativa spp. indica）基因型材料，通过多样性阵列技术（DArT）测序平台完成27560个SNP位点的基因分型。其中近66%的SNP位点具有多态性，15020个多态性SNP被定位至水稻12条染色体上。籼稻、粳稻、ARICA及NERICA类群内基因型间的遗传距离范围分别为0.016~0.623、0.020~0.692、0.075~0.763及0.014~0.644。遗传距离大于0.400的基因型对占比在NERICA类群中最高（35.1%），其次为ARICA（18.2%）、粳稻（17.4%），籼稻类群占比最低（5.6%）。本研究发现1对粳稻、11对籼稻及35对NERICA基因型的总等位基因差异率低于2%，这一现象由其中26对基因型具有相同系谱关系所致。聚类分析、主成分分析及基于模型的群体结构分析均显示，供试材料可分为两个与种植生态型对应的明显类群：低地生态型（主要包含籼稻及低地型NERICA）与旱地生态型（主要包含粳稻及旱地型NERICA）。多数种间低地型NERICA单独聚为一个亚群，这可能源于光稃稻基因组与籼稻基因组存在显著差异。分子方差分析结果表明，低地与旱地生态型间存在极强的遗传分化（FST=0.688），而31.2%的遗传变异来源于类群内部的差异。在15020个定位至染色体的SNP位点中，约8%（1197个）在低地与旱地生态型间存在显著差异（P<0.05），这些位点形成了可明确区分两类生态型的差异化单倍型。本研究是首次利用高密度分子标记对非洲广泛应用的NERICA、ARICA品种与籼、粳稻品种进行系统表征，研究结果可为水稻育种家筛选亲本、培育新型优良水稻种质提供理论支撑。