利用SSR标记与毛细管电泳对甘蔗属进行的遗传分析

为探讨甘蔗属内不同种之间的遗传多样性,利用SSR标记与毛细管电泳技术,对来自甘蔗属3个不同种的12个材料19对引物进行检测,共检测到229个DNA多态性条带,19对引物扩增的DNA条带范围集中在100～260bp之间。12个甘蔗材料的Jaccard遗传相似度,最小0.09,最大0.65,平均为0.26。通过遗传相似性系数分析,UPGMA聚类图内12个甘蔗材料可分为两个群,三个割手密种材料分为一个亚群,甘蔗栽培品种与甘蔗热带种合为一个亚群。结果表明:热带种比割手密种具有和甘蔗栽培品种更亲近的遗传关系;SSR分子标记与毛细管技术结合,相比别的分子标记技术或电泳技术,具有更准确、简便、自动化等优点。     

11份割手密遗传多样性的SSR分析

利用10对多态性丰富的SSR引物,以国家甘蔗种质资源圃中保存的14份具有代表性的割手密为对照,对未收集过的云南地区11份割手密（Saccharum spontaneum L.）野生资源进行多样性分析。结果共扩增出233条DNA谱带,与对照相比,新采集材料的多态性条带为207条,其中14条为特有条带,多态性条带比率为0.89。遗传相似性系数和UPGMA聚类分析表明,新采集的材料并没有单独聚为一类,而是比较分散,在相似性系数为0.64处做切割线,参试材料可分为三个类群：第一类群主要由龙门割手密、河边村割手密和福建仙游1号组成;第二类群中包含19份材料,其中新采集的样品有上岗割手密、他拉割手密、安乐割手密、勐根割手密、芒美割手密、贺海割手密、回落割手密、里拉割手密和曼亨割手密,对照材料主要包含了云南、四川、越南、老挝、泰国地区的割手密,其共同特点是均分布在内陆地区;第三类群包括3个材料,分别是海南1号、海南92-2和广东化州割手密,其中不包含新采集的材料。而在相似性系数为0.654处作切割线又能将上述第二类群分为较细的三个亚群。由此可见,新采集的11份割手密资源具有丰富的遗传多样性,与已收集的资源相比,具有一定的差异性。说明依靠云南高山峡谷等立体气候特点,分布着遗传差异显著的割手密无性系。     

29份云南甘蔗创新种质的SSR遗传多样性分析和指纹图谱构建

该研究以16份甘蔗骨干亲本为参照,对29份云南甘蔗创新种质进行SSR指纹图谱构建和遗传多样性分析,以明确创新种质与16份亲本间的遗传基础和多样性水平。结果表明:6对引物共扩增出104条带,其中101条为多态性条带,多态性条带比例为97.25%;45份材料的遗传相似性系数为0.235 3~0.891 3,平均值为0.563 3;其中16份甘蔗骨干亲本的遗传相似性系数为0.301 6~0.755 6,甘蔗创新种质与甘蔗骨干亲本的特异条带比例为14∶1,涵盖了割手密、大茎野生种、斑茅和滇蔗茅等基因源。根据骨干亲本间的相似性系数范围,在相似性系数为0.43处,可将种质分为6大类群,亲缘关系相对较远,适宜作为种质间的杂交利用。通过引物区分效率分析,6对引物扩增的多态信息量为0.967 9~0.975 8,其中MSSCIR21引物区分效率最高,利用MSSCIR21和SMC1047HA引物组合构建了云南甘蔗创新种质标准指纹图谱,在相似性系数为0.85处即可区分所有种质,图谱的鉴别准确率为100%,每份资源都有唯一的指纹图谱,可将29份创新种质和16份骨干亲本区分鉴别出来。该研究能够为后续杂交利用、种质鉴定和知识产权保护提供依据。     

斑茅割手密复合体杂交利用过程野生特异基因遗传分析

揭示斑茅割手密复合体在杂交利用过程中的斑茅、割手密野生特异基因在各世代的遗传规律,为利用斑割复合体创制甘蔗育种新亲本提供理论依据。利用AFLP-PCR分子标记结合毛细管电泳技术对斑割复合体在杂交利用过程中的斑茅、割手密野生特异基因在各世代的传递动态进行分析,并研究它们之间的遗传关系。29对AFLP引物组合共扩增出3695个位点,多态性比例为97.89%。斑茅和割手密对斑割复合体的遗传贡献率分别为43.96%和56.04%。斑茅特异位点在F1、BC1和BC2 3个世代的平均遗传率分别为8.25%、1.90%和0.63%,割手密特异位点在F1、BC1和BC2 3个世代的平均遗传率分别为16.98%、2.40%和0.21%,特异遗传物质均呈逐代减少趋势。比较不同世代甘蔗栽培种亲本遗传到后代的特异位点比率,F1的GT02-761特异位点比率最高,BC1的GT05-2743特异位点比例平均高达92.75%,BC2的ROC23遗传率最低,为49.09%,FN39遗传率最高,达94.32%。聚类分析结果表明斑割复合体偏向父本遗传,斑割复合体杂交后代偏向甘蔗栽培种遗传,与分子遗传关系分析结果一致。研究表明,经过3代的遗传重组,斑割复合体后代的遗传物质与斑割复合体相比已发生了很大的改变;研究明确了斑茅、割手密2个亲本在3个世代的遗传贡献规律,为进一步的杂交选育提供理论支持。     

割手密野生资源抗逆性研究进展

割手密作为现代甘蔗遗传杂交育种史上最为成功的野生亲本,对多种不良环境都具有很强的抗逆性,被公认为是抗逆基因的主要来源。但目前真正被有效利用的割手密抗逆亲本和抗逆基因非常有限,我国自育和引进甘蔗主栽品种的抗逆性仍然比较单一且普遍偏弱,因此加强割手密优良抗逆亲本筛选和抗逆基因挖掘利用研究意义重大。本文综述了不同基因型割手密在非生物逆境(干旱、低温等理化因素)和生物逆境(病虫害侵染)下的抗逆性鉴定及其抗逆基因克隆和功能验证等国内外相关研究进展;并探讨了当前割手密资源抗逆材料筛选和抗逆基因挖掘利用中存在的问题和今后的研究方向,希望为高效利用割手密优异抗逆基因资源开展甘蔗多抗逆性聚合育种提供参考。     

80份甘蔗种质RAMP标记遗传多样性分析

采用RAMP分子标记技术对80份甘蔗种质(32份祖亲种、48份栽培品种或品系)的遗传基础进行了分析。从30对引物组合中筛选出4对多态性较强引物,构建了甘蔗80份种质的RAMP指纹图谱,这四对引物组合共扩增出84条带,其多态性为91.7%。80份种质的遗传相似系数变化范围在0.433～0.988,平均0.710。聚类分析表明,随着相似系数结合线的不同,可分别将参试的甘蔗种质从属间(甘蔗属与斑茅种)、野生种(割手密种、大茎野生种、印度种、中国种)与栽培种(热带种)间、栽培种与杂交栽培品种(或品系)间区别开来。各祖亲种与杂交栽培品种(或品系)的遗传相似性由大到小依次为热带种>印度种和中国种>大茎野生种＞云南割手密种＞其它割手密种＞斑茅。另外,本试验首次利用RAMP标记,获得了部分热带种、野生种及斑茅种特异片段,并发现这些特异片段能不同程度地在具有其血缘的栽培种中得到传递。     

甘蔗与斑茅割手密复合体杂交后代的分子标记鉴定

为有效利用甘蔗野生种质拓宽甘蔗遗传基础,本研究利用甘蔗与斑茅割手密复合体进行杂交,同时应用序列相关扩增多态性(SRAP)和微卫星(SSR)分子标记技术鉴定其后代。两种分子标记鉴定结果相互印证表明:3个杂交组合的后代中,经表型鉴定含斑茅血缘的34个后代为真杂种。该真杂种后代为进一步综合利用斑茅、割手密的优异基因改良甘蔗品种提供了优良的创新种质。     

云南甘蔗常用亲本资源遗传多样性的SSR分析

以63份云南育种机构常用的亲本资源为研究对象,10份原始亲本种为外群体,使用30对多态性较高,在甘蔗遗传连锁图谱上分布较为广泛的Genomic-SSR引物对云南常用亲本资源开展遗传多样性评价。结果表明：云南常用亲本在30个SSR位点上表现出丰富的多态性,共获得363个扩增条带,其中多态性条带数为352个,平均多态性条带比例和多态信息量分别为96.97%和0.9441;从常用亲本的来源地区来看,大陆亲本的多样性要高于国外亲本和台湾亲本;在Jaccard相似性系数方面,云南常用亲本材料之间的相似性系数范围在0.2804-0.7329之间,平均为0.4309,表现出较大的遗传差异,其中来自大陆地区的亲本遗传差异最大,其次为来自国外地区的亲本;UPGMA聚类分析将所有亲本材料分为一大一小两个类群, 而大类群又可分为2个亚类群,中国大陆地区一些即是主栽品种又是亲本的材料表现出较近的亲缘关系,而引自国外的大部分亲本和一些老的国内自育亲本也表现出较近的亲缘关系。以上结果将为上述亲本资源的高效利用奠定了良好的基础,并为全国育种机构在亲本选择和组合配置提供重要参考。     

甘蔗杂交品种核心种质重要农艺性状评价及亲缘关系分析

以107份甘蔗杂交品种核心种质为研究材料,ROC22为对照品种,通过新植和宿根2年的田间试验,对蔗茎公顷产量、甘蔗蔗糖分、公顷含糖量等性状进行最小显著差数法(LSD)两两比较和Duncan多重比较评价,筛选优异材料,利用SSR分子标记建立优异材料与我国骨干亲本的亲缘关系。结果表明36份材料在蔗茎公顷产量、甘蔗蔗糖分、公顷含糖量等指标上优于对照品种,可作为亲本进行杂交,且蔗茎公顷产量对公顷含糖量的影响远大于甘蔗蔗糖分对公顷含糖量的影响;20对SSR引物扩增得到292个标记,其中283个为多态性标记;优异材料与我国骨干亲本相似性系数范围在0.384~0.590之间,平均为0.437,存在较大的遗传差异;UPGMA聚类可将所有材料划分为5个类群,蔗茎公顷产量和公顷含糖量表现优异的材料在各类群都有分布,甘蔗蔗糖分表现优异的材料主要集中在Ⅱ、Ⅲ、Ⅳ类群,Ⅲ类群更集中;本研究为甘蔗种质创新、遗传育种提供了优异亲本材料,为杂交组合的配制提供重要指导。     

利用SSR与RAPD分子标记评估甘蔗品种的遗传多样性

利用SSR与RAPD两种分子标记对美国、中国台湾以及中国大陆不同甘蔗育种单位选育的甘蔗品种或亲本材料的遗传多样性进行评估。其中19对SSR引物共扩增出87条带,多态性带为84条,多态性比例为96.55%,扩增出的条带数范围为2~8条,平均每对引物扩增出4.58条带,引物的PIC值范围为0.34~0.93,平均0.64。21条RAPD引物共扩增出184条带,扩增条带数范围为3~16,平均每条引物扩增8.76条带,其中多态性带为184,多态性比例为100%,引物PIC范围为0.53~0.97,平均0.86。结果表明,两种分子标记都能较好的评估甘蔗品种的遗传多样性。     

Biochemical genetic markers in sugarcane

Summary Isozyme variation was used to identify biochemical markers of potential utility in sugarcane genetics and breeding. Electrophoretic polymorphism was surveyed for nine enzymes among 39 wild and noble sugarcane clones, belonging to the species most closely related to modern varieties. Up to 114 distinct bands showing presence versus absence type of variation were revealed and used for qualitative characterization of the materials. Multivariate analysis of the data isolated the Erianthus clone sampled and separated the Saccharum spontaneum clones from the S. robustum and S. officinarum clones; the latter two were not differentiated from one another. The analysis of self-progenies of a 2n=112 S. spontaneum and of a commercial variety showed examples of mono- and polyfactorial segregations. Within the progeny of the variety, co-segregation of two isozymes frequent in S. spontaneum led to them being assigned to a single chromosome initially contributed by a S. spontaneum donor. This illustrates how combined survey of ancestral species and segregation analysis in modern breeding materials should permit using the lack of interspecific cross-over to establish linkage groups in a sugarcane genome.     

Evaluation of the cold tolerance of Saccharum spontaneum L. clones with different ploidy levels on the basis of morphological and physiological indices

• Saccharum spontaneum L. is one of the most important germplasm resources for modern sugarcane breeding. Exploring the cold tolerance of S. spontaneum clones with different ploidy levels and screening for cold‐tolerant material can be helpful in parent selection for breeding cold‐tolerant sugarcane.
• Morphological indices, leaf ultrastructure and physiological indices were used to evaluate the cold tolerance of 36 S. spontaneum clones with different ploidy levels (2n = 40, 48, 54, 60, 64, 78, 80, 88, 92 and 96).
• The morphological indices of S. spontaneum clones with different ploidy levels were positively correlated with ploidy. Under low‐temperature stress, the chloroplast and mitochondrial structures of the clones with high ploidy were more severely damaged than were those of clones with low ploidy. A comprehensive evaluation of the physiological indices showed that the 36 S. spontaneum clones could be divided into four categories: strongly cold tolerant, cold tolerant, moderately cold tolerant and cold sensitive. Correlation analysis of the morphological indices and cold tolerance revealed a significant negative correlation between cold tolerance and ploidy. On the basis of the morphological and physiological indices, optimal stepwise regression equations that can be used for the selection of cold‐tolerant S. spontaneum resources were established.
• The S. spontaneum clones with low ploidy are more cold tolerant than those with high ploidy. Clones 12‐37, 13‐10 and 12‐23 are strongly cold‐tolerant germplasm resources, which suggests these germplasm sources have high potential for use in breeding cold‐tolerant sugarcane.

     

Phylogenetic Analysis of Different Ploidy Saccharum spontaneum Based on rDNA-ITS Sequences

Saccharum spontaneum L. is a crucial wild parent of modern sugarcane cultivars whose ploidy clones have been utilized successfully in improving the stress resistance and yield related traits of sugarcane cultivars. To establish knowledge regarding the genetic variances and evolutional relationships of ploidy clones of Saccharum spontaneum collected in China, the rDNA-ITS sequences of 62 ploidy clones including octaploid clones (2n = 64), nonaploid clones (2n = 72), decaploid clones (2n = 80), and dodecaploid clones (2n = 96), were obtained and analyzed. The rDNA-ITS sequences of four species from Saccharum and Sorghum bicolor selected as controls. The results showed that decaploid clones (2n = 80) possess the most abundant variances with 58 variable sites and 20 parsim-informative sites in ITS sequences, which were then followed by octaploid clones with 43 variable sites and 17 parsim-informative sites. In haplotype diversity, all four population exhibited high diversity, especially nonaploid and decaploid populations. By comparing the genetic distances among four ploidy populations, the dodecaploid population exhibited the closest relationship with the nonaploid population, and then the relationship strength decreased successively for the decaploid population and then for the octaploid population. Population differentiation analysis showed that the phenomena of population differentiation were not found among different ploidy populations, and low coefficient of gene differentiation(Gst) and high gene flow(Nm) occur among these populations possessing close genetic relationship. These results mentioned above will contribute to the understanding of the evolution of different ploidy populations of Saccharum spontaneum and provide vital knowledge for their utilization in sugarcane breeding and innovation.     

Quantitative analysis of the effect of selection history on sugar yield adaptation of sugarcane clones

An objective of the CSR sugarcane breeding programme in Australia was to assess the scope for broadening the genetic base of the commercial sugarcane germ plasm through interspecific hybridization with Saccharum spontaneum clones. The contribution of both selection history and S. spontaneum to sugar yield and its components was investigated in the germ plasm pool assembled. The analysis was conducted on a data-set of 256 clones, consisting of parents and full-sib families generated from 32 biparental crosses, tested in six environments. The minimum number of generations back to S. spontaneum ancestor in the clone's pedigree was used as a germ plasm score. The geographical origin and selection history of each parent and their use in the biparental crosses were used to develop a selection history score for parents and offspring. The variation for seven attributes, cane yield, commercial cane sugar %, sugar yield, stalk number per stool, stalk weight, fibre % and ash % juice was partitioned according to the germ plasm and selection history scores. Significant (P<0.05) clone variation and clone x environment interaction for all attributes was present. The germ plasm scores accounted for a significant (P<0.05) component of the clone variation for all of the attributes except cane yield. There was an increase in sugar yield with an increase in the minimum number of generations back to a S. spontaneum clone. The selection history groups accounted for a high proportion of the variation among parental clones for all of the attributes except cane yield. This suggested that parents were the outcome of strong selection pressure for the commercial cane attributes. However, the selection history groups for the offspring produced by random mating of parents did not account for a high proportion of the variation for the attributes. Using the mixture method of classification we partitioned the 256 clones into five groups for patterns of performance for the seven attributes across the six environments. The five groups emphasized major differences in the patterns of performance for the seven attributes across environments. The distribution of germ plasm and selection history scores in each of the five groups indicated that their patterns of performance were associated with selection history and minimum generations to S. spontaneum. Therefore, both the analysis on selection history and germ plasm scores (extrinsic classification) and the analysis on the mixture method of classification (intrinsic classification) emphasized the influence of selection history on the sugar yield of sugarcane.     

Features of SNP and SSR diversity in a set of ICARDA barley germplasm collection

Detection and utilization of genetic variation available in the germplasm collection for crop improvement have been the prime activities of breeders. Here a set of ICARDA barley germplasm collection comprising of 185 cultivated (Hordeum vulgare L.) and 38 wild (H. spontaneum L.) genotypes originated from 30 countries of four continents was genotyped with 68 single nucleotide polymorphism (SNP) and 45 microsatellite or simple sequence repeat (SSR) markers derived from genes (expressed sequence tags, ESTs). As two SNP markers provided 2 and 3 datapoints, a total of 71 SNPs were surveyed that yielded a total of 143 alleles. The number of SSR alleles per locus ranged from 3 to 22 with an average of 7.9 per marker. Average PIC (polymorphism information content) value for SSR and SNP markers were recorded as 0.63 and 0.38, respectively. Heterogeneity was recorded at both SNP and SSR loci in an average of 5.72 and 12.42% accessions, respectively. Genetic similarity matrices for SSR and SNP allelic data were highly correlated (r = 0.75, P < 0.005) and therefore allelic data for both markers were combined and analyzed for understanding the genetic relationships among the germplasm surveyed. Majority of clusters/subclusters were found to contain genotypes from the same geographic origins. While comparing the genetic diversity, the accessions coming from Middle East Asia and North East Asia showed more diversity as compared to that of other geographic regions. Majority of countries representing Africa, Middle East Asia, North East Asia and Arabian Peninsula included the genotypes that contained rare alleles. As expected, spontaneum accessions, as compared to vulgare accessions, showed a higher number of total alleles, higher number of alleles per locus, higher effective number of alleles and higher allelic richness and a higher number of rare alleles were observed. In summary, the examined ICARDA germplasm set showed ample natural genetic variation that can be harnessed for future breeding of barley as climate change and sustainability have become important throughout all growing areas of the world, drought/heat tolerance being the most important ones.     

Expression of the Grifola frondosa Trehalose Synthase Gene and Improvement of Drought-Tolerance in Sugarcane （Saccharum officinarum L.）

Trehalose Is a nonreduclng dlsaccharlde of glucose that functions as a protectant In the stabilization of blologlcal structures and enhances stress tolerance to abiotic stresses in organisms. We report here the expression of a Grlfola frondosa trehalose synthase （TSase） gene for Improving drought tolerance In sugarcane （Saccharum offlclnarum L.）. The expression of the transgene was under the control of two tandem copies of the CaMV35S promoter and transferred Into sugarcane by Agrobacterium tumefaciens EHA105. The transgenlc plants accumulated high levels of trehalose, up to 8.805-12.863 mg/g fresh weight, whereas It was present at undetectable level in nontransgenlc plants. It has been reported that transgenlc plants transformed with Escherlchla coil TPS （trehalose-6-phosphatesynthase） and/or TPP （trehalose-6-phosphate phosphatase） are severely stunted and have root morphologlc alterations. Interestingly, our transgenlc sugarcane plants had no obvious morphological changes and no growth Inhibition in the field. Trehalose accumulation in 35S-35S：TSase plants resulted In In- creased drought tolerance, as shown by the drought and the drought physiological Indexes, such as the rate of bound water/free water, plasma membrane permeability, malondlaldehyde content, chlorophyll a and b contents, and activity of SOD and POD of the excised leaves. These results suggest that transgenlc plants transformed with the TSase gene can accumulate high levels of trehalose and have enhanced tolerance to drought.     

An Assessment of the Phylogenetic Relationship Among Sugarcane and Related Taxa Based on the Nucleotide Sequence of 5S rRNA Intergenic Spacers

5S rRNA intergenic spacers were amplified from two elite sugarcane (Saccharumhybrids) cultivars and their related taxa by polymerase chain reaction (PCR) with 5S rDNA consensus primers. Resulting PCR products were uniform in length from each accession but exhibited some degree of length variation among the sugarcane accessions and related taxa. These PCR products did not always cross hybridize in Southern blot hybridization experiments. These PCR products were cloned into a commercial plasmid vector PCR™ 2.1 and sequenced. Direct sequencing of cloned PCR products revealed spacer length of 231–237 bp for S. officinarum, 233–237 for sugarcane cultivars, 228–238 bp for S. spontaneum, 239–252 bp for S. giganteum, 385–410 bp for Erianthusspp., 226–230 bp for Miscanthus sinensisZebra, 206–207 bp for M. sinensisIMP 3057, 207–209 bp for Sorghum bicolor, and 247–249 bp for Zea mays. Nucleotide sequence polymorphism were found at both the segment and single nucleotide level. A consensus sequence for each taxon was obtained by Align X. Multiple sequences were aligned and phylogenetic trees constructed using Align X, CLUSTAL and DNAMAN programs. In general, accessions of the following taxa tended to group together to form distinct clusters: S. giganteum, Erianthusspp., M. sinensis, S. bicolor, and Z. mays. However, the two S. officinarumclones and two sugarcane cultivars did not form distinct clusters but interrelated within the S. spontaneumcluster. The disclosure of these 5S rRNA intergenic spacer sequences will facilitate marker-assisted breeding in sugarcane. This revised version was published online in July 2006 with corrections to the Cover Date.     

Correlation between hordatine accumulation, environmental factors and genetic diversity in wild barley (Hordeum spontaneum C. Koch) accessions from the Near East Fertile Crescent

Wild barley shows a large morphological and phenotypic variation, which is associated with ecogeographical factors and correlates with genotypic differences. Diversity of defense related genes and their expression in wild barley has been recognized and has led to attempts to exploit genes from H. spontaneum in breeding programs. The aim of this study was to determine the variation in the accumulation of hordatines, which are Hordeum-specific preformed secondary metabolites with strong and broad antimicrobial activity in vitro, in 50 accessions of H. spontaneum from different habitats in Israel. Differences in the accumulation of hordatines in the seedling stage were significant between different H. spontaneum genotypes from different regional locations and micro-sites. Variation in the hordatine accumulation within genotypes was between 9% and 45%, between genotypes from the same location between 13% and 38%, and between genotypes from different locations up to 121%. Principal component analysis showed that water related factors explain 39%, temperature related factors explain 33% and edaphic factors account for 11% of the observed variation between the populations of H. spontaneum. Genetic analysis of the tested accessions with LP-PCR primers that are specific for genes involved in the biosynthetic pathway of hordatines showed tight correlations between hordatine abundance and genetic diversity of these markers. Multiple regression analyses indicated associations between genetic diversity of genes directly involved in hordatine biosynthesis, ecogeographical factors and the accumulation of hordatines.     

Target enrichment sequencing of 307 germplasm accessions identified ancestry of ancient and modern hybrids and signatures of adaptation and selection in sugarcane (Saccharum spp.), a ‘sweet’ crop with ‘bitter’ genomes

Sugarcane (Saccharum spp.) is a highly energy‐efficient crop primarily for sugar and bio‐ethanol production. Sugarcane genetics and cultivar improvement have been extremely challenging largely due to its complex genomes with high polyploidy levels. In this study, we deeply sequenced the coding regions of 307 sugarcane germplasm accessions. Nearly five million sequence variations were catalogued. The average of 98× sequence depth enabled different allele dosages of sequence variation to be differentiated in this polyploid collection. With selected high‐quality genome‐wide SNPs, we performed population genomic studies and environmental association analysis. Results illustrated that the ancient sugarcane hybrids, S. barberi and S. sinense, and modern sugarcane hybrids are significantly different in terms of genomic compositions, hybridization processes and their potential ancestry contributors. Linkage disequilibrium (LD) analysis showed a large extent of LD in sugarcane, with 962.4 Kbp, 2739.2 Kbp and 3573.6 Kbp for S. spontaneum, S. officinarum and modern S. hybrids respectively. Candidate selective sweep regions and genes were identified during domestication and historical selection processes of sugarcane in addition to genes associated with environmental variables at the original locations of the collection. This research provided an extensive amount of genomic resources for sugarcane community and the in‐depth population genomic analyses shed light on the breeding and evolution history of sugarcane, a highly polyploid species.     

Very close relationship of the chloroplast genomes among Saccharum species

We recently determined the complete sequence of the sugarcane chloroplast genome. Here, we have used the information for a comprehensive phylogenetic analysis of the genus Saccharum, using all six species (13 accessions). The polymorphisms between sugarcane and maize in 26 chloroplast genome regions were used for the analysis. In 18 of the 26 regions (a total of 5,381 bp), we found 41 mutations involving 17 substitutions, three inversions, six insertion/deletion mutations, and 15 simple sequence repeat length polymorphisms. Based on these results, we calculated a phylogenetic tree of the genus Saccharum, in which all six species are clearly separated. By the analysis, (1) S. sinense and S. barberi, which have identical sequences, belong to the same clade, whereas the other four species, S. officinarum, S. robustum, S. edule, and S. spontaneum, form an independent clade; (2) S. spontaneum has a paraphyletic relationship with the other five species; and (3) no or very low intraspecific variation was observed in S. officinarum, S. robustum, S. sinense, S. barberi, and S. edule, whereas higher intraspecific variation was observed in S. spontaneum. Based on the number of nucleotide substitutions, the divergence time between S. officinarum and S. spontaneum, and between S. officinarum and maize were calculated to be about 730–780 thousand years ago and about 5.9 million years ago, respectively. These results suggest that the cytoplasm of Saccharum species are very closely related.