Table_1.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（Africa Rice Center）的水稻育种团队以光稃稻（Oryza glaberrima Steud.）为供体亲本、亚洲栽培稻（Oryza sativa L.）为轮回亲本开展种间杂交，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。
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（single nucleotide polymorphisms, SNPs）标记，解析非洲地区330个广泛应用的水稻基因型（genotypes）的遗传变异、亲缘关系与群体结构。
本研究共对11份ARICA材料、85份NERICA材料、62份亚洲栽培稻粳亚种（O. sativa spp. japonica）及172份亚洲栽培稻籼亚种（O. sativa spp. indica）材料进行基因分型，使用27560个SNPs标记，依托DArTseq平台完成分型。其中近66%的SNPs具有多态性，15020个多态性SNPs被定位到水稻12条染色体上。
籼稻、粳稻、ARICA及NERICA类群的基因型对间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的基因型对比例在NERICA类群中最高（占总对数的35.1%），其次为ARICA（18.2%）、粳稻（17.4%）与籼稻（5.6%）。本研究发现1对粳稻、11对籼稻及35对NERICA材料的总计分等位基因差异小于2%，该现象源于其中26对材料具有完全一致的系谱。
聚类分析、主成分分析（principal component analysis）及基于模型的群体结构分析均揭示出两个显著类群，分别对应低地种植生态型（主要包含籼稻与低地NERICA）和旱地种植生态型（主要包含粳稻与旱地NERICA）。大部分种间低地NERICA材料单独形成一个亚群，这可能是由于光稃稻基因组与籼稻基因型存在差异所致。分子方差分析（analysis of molecular variance）结果显示，低地与旱地生态型间存在极强的遗传分化（遗传分化系数FST=0.688），且31.2%的遗传变异来源于类群内部。在15020个已定位的SNPs中，约8%（1197/15020）的标记在低地与旱地生态型间存在显著差异（P<0.05），这些标记所形成的对立单倍型（haplotypes）可清晰区分低地与旱地水稻基因型。
本研究是首次利用高密度标记对非洲广泛应用的籼、粳稻品种与NERICA、ARICA品种进行遗传特征解析的研究，研究结果可为水稻育种家开展亲本选择以培育新型改良水稻种质资源（germplasm）提供重要参考。