Allopolyploid origin and niche expansion of Rhodiola integrifolia(Crassulaceae)

Polyploidy after hybridization between species can lead to immediate post-zygotic isolation,causing saltatory origin of new species.Although the incidence of polyploidization in plants is high,it is thought that a new polyploid lineage can succeed only if it establishes a new ecological niche divergent from its progenitor lineages.We tested the hypothesis that Rhodiola integrifolia from North America is an allopolyploid produced by R. rhodantha and R.rosea and determined whether its survival can be explained by the niche divergence hypothesis.To this end,we sequenced two low-copy nuclear genes(ncpGS and rpb2) in a phylogenetic analysis of 42 Rhodiola species and tested for niche equivalency and similarity using Schoener’s D as the index of niche overlap.Our phylogeny-based approach showed that R integrifolia possesses alleles from both R. rhodantha and rosea Dating analysis showed that the hybridization event that led to R.integrifolia occurred ca.1.67 Mya and niche modeling analysis showed that at this time,both R.rosea and R.rhodantha may have been present in Beringia,providing the opportunity for the hybridization event.We also found that the niche of R.integrifolia differs from that of its progenitors in both niche breadth and optimum.Taken together,these results confirm the hybrid origin of R.integrifolia and support the niche divergence hypothesis for this tetraploid species.Our results underscore the fact that lineages with no current overlapping distribution could produce hybrid descendants in the past,when climate oscillations made their distributions overlap.

Identification of MAM1s in Regulation of 3C Glucosinolates Accumulation in Allopolyploid Brassica juncea

Allopolyploid Brassica juncea is particularly enriched in sinigrin,a kind of 3C aliphatic glucosinolates(GSLs),giving rise to characteristic taste after picking.However,the molecular mechanism underlying 3C aliphatic GSLs biosynthesis in this species remains unknown.In this study,we genome-widely identified GSLs metabolic genes,indicating different evolutionary rate of GSLs metabolic genes between subgenomes of B.juncea.Eight methythioalkylmalate synthase(MAMs)homologs were identified from B.juncea,in which six MAM1s were located in chloroplast and the other two were not detected with any expression.Furthermore,BjMAM1-4,BjMAM1-5,and BjMAM1-6 displayed higher expression levels in leaves than other tissues.Silenced expression analysis revealed that BjMAM1-4 and BjMAM1-6 function in 3C and 4C aliphatic GSLs accumulation.The specificity of the substrate selection for the second cycle reaction is much lower than that of the first cycle,suggesting these genes may preferentially catalyze 3C aliphatic GSLs biosynthesis.Our study provides insights into the molecular mechanism underlying the accumulation of 3C aliphatic GSLs,thereby facilitating the manipulation of aliphatic GSLs content in B.juncea.

The occurrence,inheritance,and segregation of complex genomic structural variation in synthetic Brassica napus

"Synthetic"allopolyploids recreated by interspecific hybridization play an important role in providing novel genomic variation for crop improvement.Such synthetic allopolyploids often undergo rapid genomic structural variation(SV).However,how such SV arises,is inherited and fixed,and how it affects important traits,has rarely been comprehensively and quantitively studied in advanced generation synthetic lines.A better understanding of these processes will aid breeders in knowing how to best utilize synthetic allopolyploids in breeding programs.Here,we analyzed three genetic mapping populations(735 DH lines)derived from crosses between advanced synthetic and conventional Brassica napus(rapeseed)lines,using whole-genome sequencing to determine genome composition.We observed high tolerance of large structural variants,particularly toward the telomeres,and preferential selection for balanced homoeologous exchanges(duplication/deletion events between the A and C genomes resulting in retention of gene/chromosome dosage between homoeologous chromosome pairs),including stable events involving whole chromosomes("pseudoeuploidy").Given the experimental design(all three populations shared a common parent),we were able to observe that parental SV was regularly inherited,showed genetic hitchhiking effects on segregation,and was one of the major factors inducing adjacent novel and larger SV.Surprisingly,novel SV occurred at low frequencies with no significant impacts on observed fertility and yield-related traits in the advanced generation synthetic lines.However,incorporating genome-wide SV in linkage mapping explained significantly more genetic variance for traits.Our results provide a framework for detecting and understanding the occurrence and inheritance of genomic SV in breeding programs,and support the use of synthetic parents as an important source of novel trait variation.

Rapid changes of microsatellite flanking sequence in the allopolyploidization of new synthesized hexaploid wheat

It was suggested that the rapid changes of DNA sequence and gene expression oc- curred at the early stages of allopolyploid formation. In this study, we revealed the microsatellite (SSR) differences between newly formed allopolyploids and their donor parents by using 21 primer sets specific for D genome of wheat. It was indicated that rapid changes had occurred in the “shock” process of the allopolyploid formation between tetraploid wheat and Aegilops tauschii. The changes of SSR flanking sequence resulted in appearance of novel bands or disappearance of parental bands. The disappearance of the parental bands showed much higher frequencies in comparison with that of appearance of novel bands. Disappearance of the parental bands was not random. The frequency of disappearance in tetraploid wheat was much higher than in Ae. tauschii, i. e. the disappearance frequency in AABB genome was much higher than in D genome. Changes of SSR flanking sequence occurred at the early stage of F1 hybrid or just after chro- mosome doubling. From the above results, it can be inferred that SSR flanking sequence region was very active and was amenable to change in the process of polyploidization. This suggested that SSR flanking sequence probably had special biological function at the early stage of ploy- ploidization. The rapid and directional changes at the early stage of polyploidization might con- tribute to the rapid evolution of the newly formed allopolyploid and allow the divergent genomes to act in harmony.

Genome evolution in allopolyploid wheat—a revolutionary reprogramming followed by gradual changes

Allopolyploidy accelerates genome evolution in wheat in two ways： 1） allopolyploidization triggers rapid genome alterations （revolutionary changes） through the instantaneous generation of a variety of cardinal genetic and epigenetic changes, and 2） the allopolyploid condition facilitates sporadic genomic changes during the life of the species （evolutionary changes） that are not attainable at the diploid level. The revolutionary alterations, occurring during the formation of the allopolyploid and leading to rapid cytological and genetic diploidization, facilitate the successful establishment of the newly formed allopolyploid in nature. On the other hand, the evolutionary changes, occurring during the life of the allopolyploids, increase the intra-specific genetic diversity, and consequently, increased fimess, adaptability and competitiveness. These phenomena, emphasizing the dynamic plasticity of the allopolyploid wheat genome with regards to both structure and function, are described and discussed in this review.

Expression of CENH3 alleles in synthesized allopolyploid Oryza species

Synthesized allopolyploids are valuable materials for comparative analyses of two or more distinct genomes, such as the expression changes （activation, inactivation or differential expression） of orthologous genes following allopolyploidization. CENH3 is a centromerespecific histone H3 variant and has been regarded as a central component in kinetochore formation and centromere function. In this study, interspecific hybrids of Oryza genus （AA × CC, AA × CCDD） and their backcross progenies were produced, and the genome constitutions were identified as AC, ACC, ACD, AACD, or AA（CD） by Genomic in situ hybridization （GISH）. We further cloned and sequenced the CENH3 genes from O. sativa （AA）, O. officinalis （CC） and O. latifolia （CCDD）. Sequencing of RT-PCR products revealed that CENH3_C2 and CENH3_D, the two CENH3 alleles from O. latifolia, showed polymophism in several sites, while CENH3_C2 and CENH3_C1 from O. officinalis were different at only two amino acids positions. Moreover, we found that the CENH3 genes from both parents are expressed in interspecific hybrids and their progenies. Specifically, based on our cDNA sequencing data, the ratio of expres- sion level between CENH3_A and CENH3_C1 was approximately 1 in AC and 0.5 in ACC genomes, respectively. As a result, the CENH3 expression patterns shed more light on the inter-coordination between varied centromeric DNA sequences and highly conserved kinetochore protein in synthesized allopolyploids of Oryza genus.

Comparative effect of allopolyploidy on transposable element composition and gene expression between Gossypium hirsutum and its two diploid progenitors

An allopolyploidization event formed allotetraploid Gossypium species from an A-genome diploid species and a D-genome diploid species. To explore the responses of transposable elements(TEs) to allopolyploidy, we assembled parallel TE datasets from G. hirsutum, G. arboreum and G. raimondii and analyzed the TE types and the effects of TEs on orthologous gene expression in the three Gossypium genomes.Gypsy was the most abundant TE type and most TEs were located $500 bp from genes in all three genomes. In G. hirsutum, 35.6% of genes harbored TE insertions, whereas insertions were more frequent in G. arboreum and G. raimondii. G. hirsutum had the highest proportion of uniquely matching 24-nt small interfering RNAs(siRNAs) that targeted TEs. TEs,particularly those targeted by 24-nt siRNAs, were associated with reduced gene expression, but the effect of TEs on orthologous gene expression varied substantially among species. Orthologous gene expression levels in G. hirsutum were intermediate between those of G. arboreum and G. raimondii, which did not experience TE expansion or reduction resulting from allopolyploidization. This study underscores the diversity of TEs co-opted by host genes and provides insights into the roles of TEs in regulating gene expression in Gossypium.

The allopolyploid B. juncea genome uncovered differential homoeolog gene expression influencing selection

With the long-term support by the National Natural Science Foundation of China,Ministry of Agriculture,and Science and Technology Department of Zhejiang Province,the research team led by Prof.Zhang Mingfang(张明方)at Zhejiang University,assembled an allopolyploid B.juncea genome and uncovered differential homoeolog gene expression influencing selection,which was published in Nature

Genome-wide recombination variation in biparental segregating and reciprocal backcross populations provides information for introgression breeding in Brassica napus

Variation in patterns of recombination in plant genomes provides information about species evolution,genetic diversity and crop improvement. We investigated meiotic crossovers generated in biparental segregating and reciprocal backcross populations of the allopolyploid genome of rapeseed(Brassica napus)(AACC, 2n = 38). A structured set of 1445 intercrossed lines was derived from two homozygous de novo genome-assembled parents that represented the major genetic clusters of semi-winter Chinese and winter European rapeseeds, and was used to increase QTL resolution and achieve genomic reciprocal introgression. A high-density genetic map constructed with 6161 genetic bins and anchored centromere regions was used to establish the pattern of recombination variation in each chromosome. Around 93%of the genome contained crossovers at a mean rate of 3.8 c M Mb^(-1), with the remaining 7% attributed to centromeres or low marker density. Recombination hotspots predominated in the A genome, including two-thirds of those associated with breeding introgression from B. rapa. Genetic background might affect recombination variation. Introgression of genetic diversity from European winter to Chinese semi-winter rapeseed showed an increase in crossover rate under the semi-winter environment. Evidence for an elevated recombination rate having historically contributed to selective trait improvement includes accumulation of favorable alleles for seed oil content on hotspots of chromosome A10. Conversely, strong artificial selection may affect recombination rate variation, as appears to be the case with a coldspot resulting from strong selection for glucosinolate alleles on A09. But the cold region would be promptly reactivated by crossing design indicated by the pedigree analysis. Knowledge of recombination hotspots and coldspots associated with QTL for 22 traits can guide selection strategies for introgression breeding between the two gene pools. These results and rich genomic resources broaden our understanding of recombination behavior in allopolyploids and may advance rapeseed genetic improvement.

甜瓜属不同倍性异源多倍体光合特性及超微结构研究

以不同倍性的甜瓜属二倍体种间杂种F_1、异源三倍体和异源四倍体为试材,比较了三者间光合特性和超微结构的差异。结果表明:与种间杂种F_1相比,异源四倍体的净光合速率(P_n)、气孔导度(G_s)、蒸腾速率(T_r)、PSⅡ电子传递量子效率(φPSⅡ)和光化学猝灭系数(qP)显著升高,并且叶绿体、线粒体、基粒和片层的数目也显著增多,表现出明显的基因组剂量效应。异源三倍体的P_n、G_s、ΦPAⅡ及线粒体和片层数目显著高于异源四倍体,表现出明显的杂种优势。

极濒危植物中华水韭休宁居群的遗传结构

采用超薄平板微型聚丙烯酰胺等电聚焦电泳方法对极濒危蕨类植物中华水韭 (Isoetessinensis)现存于安徽休宁的 5个亚居群的等位酶多样性和遗传结构进行了研究。结果表明 :中华水韭居群每位点平均等位基因数A =1.7,平均多态位点比率P =5 5 .5 6 % ,平均预期杂合度He=0 .2 0 1。居群中半数的多态位点表现为等位基因的“固定杂合” ,5个亚居群的遗传多样性无显著差异 ,但都表现出严重偏离Hardy Weinberg平衡的杂合子过量 ;其遗传变异主要发生于亚居群内 (94 .2 7% ) ,亚居群之间的遗传分化较小 (Gst=0 .0 5 73) ,亚居群间遗传一致度较高 (I =0 .96 0 - 0 .999)。我们推断这可能是由于居群构建之初的奠基者效应或者原种群曾经历了较为严重的遗传瓶颈所导致 ;此外亚居群间便利的基因交流也可能起到了很大作用 (Nm =4 .5 0 6 2 )。取自休宁居群的 75株样品由 13个专一多位点基因型 (18个位点等位酶基因型 )组成 ,亚居群及个体间高度遗传均质。本文还就中华水韭休宁野生居群濒危的遗传因素进行了探讨 ,并提出了相应的保育策略。

二十一世纪水稻育种新战略Ⅱ.利用远缘杂交和多倍体双重优势进行超级稻育种

本文论述了远缘杂交和多倍体化结合利用基因组间和多倍体杂种优势，开创水稻育种新途 径的策略。纵观水稻育种的历史，无论是常规杂交育种，还是杂交稻育种，其研究战略都是建立在有 性生殖和二倍体基础上的，归根结底，都是利用栽培稻同一基因组（Ａ基因组）内优良基因的重组以及 从野生稻向栽培稻引入少数优良基因。从作物进化趋势看，水稻是二倍体，基因组小、ＤＮＡ含量低、 染色体小，增加基因组数，提高倍性水平，利用异源多倍体杂种优势将是水稻育种新途径。针对同源 四倍体水稻结实率低的关键问题，可采取拉大亲缘关系距离、减少多价体形成，应用广亲和、无融合 生殖基因等措施，从遗传机理上提高多倍体水稻结实率。按三步实施战略；一、选用极端类型籼粳稻、 爪哇稻，诱导亚种间杂种多倍体；二、诱导亚洲栽培稻和非洲栽培稻以及非洲野生稻种间杂种多倍体； 三、诱导 ＡＡ基因组的栽培稻与其它不同基因组野生稻（ＢＢ、 ＣＣ、 ＢＢＣＣ、 ＣＣＤＤ、 ＤＤ、 ＥＥ、 ＦＦ、 ＧＧ、 ＨＨＪＪ）的种间多倍体。在实施过程中发挥一些特殊基因材料的特殊作用，如广亲和基因对于克服籼便 杂种一代不育性、特别是雌败育的作用，无融合生殖缺乏减数分裂发生和受精过程对于克服染色体配

黄瓜属不同倍性异源多倍体的形态及生理特性分析

以黄瓜属3种不同倍性异源多倍体为试验材料,比较分析它们的形态和生理特性与基因组剂量的关系,为进一步研究黄瓜属基因组剂量效应、探讨植物多倍体进化机理奠定基础。结果表明:(1)黄瓜属异源四倍体与种间杂种F1相比,其叶片厚度、主蔓直径等性状随基因组剂量的增加而增大,而果实大小、主蔓节间长以及果瘤果刺的大小随基因组剂量的增加而减小。(2)在异源三倍体中,叶片厚度和主蔓直径等表型性状也表现出一定的基因组剂量效应。(3)基因组剂量的变化会引起黄瓜属异源多倍体中叶绿素含量、POD活性以及IAAi、PA和ZR等内源激素的变化。

利用SCoT标记分析花生栽培种×A.chacoensis组合异源多倍化的早期基因组变化

【目的】研究花生属异源多倍化过程中基因组变化行为,揭示花生属多倍体进化的分子机制。【方法】采用SCoT标记对四倍体栽培种仲恺花4号和二倍体野生种A.chacoensis的种间杂种F1及早期多倍体世代(S0—S3)基因组变化时间、类型和频率进行分析。【结果】18条SCoT引物共扩增出126个位点,其中多态性位点117个,多态性比率达92.86%,在供试材料中检测出了丰富的DNA多态性;与扩增出的109条亲本条带比较,F1—S3分别丢失亲本条带28、30、10、11和10条,其中,来自父本特异性条带为16、12、7、9和9条,各自新增条带9、3、10、14和8条,说明SCoT产物早在Fl即开始发生变化,变化类型包括亲本条带的丢失、跳跃式继承和新条带的产生,在丢失的亲本条带中以父本条带为主。【结论】ATG翻译起始位点及其侧翼区域在花生种间杂交异源多倍化早期迅速发生广泛而剧烈的变化,其生物学功能可能与多倍体的进化和稳定有关;SCoT标记作为一种简单、有效和实用的新型功能型分子标记技术,可以为花生属及其它物种多倍体进化中基因组遗传变化研究提供技术支持。

花生属人工异源多倍体进化早期基因表达变化的cDNA-SCoT分析

为了探索花生属异源多倍体进化理论和种间杂交过程所涉及的遗传机制,以四倍体栽培种花生与二倍体野生种A.doigoi及其种间杂种F1和早期多倍体世代（S0~S3）为材料,采用cDNA-SCoT技术研究花生属人工异源多倍体进化早期基因表达变化规律。12条SCoT引物共扩增出108个cDNA片段,获得差异片段80个,占扩增总条带数的74.07%,对其中的35个差异片段进行克隆测序,有26个和GenBank数据库中已录入的基因具有较高的相似性,包括能量与代谢相关基因（8个）、未知功能蛋白基因（3个）、抗逆性相关基因（4个）、信号传导相关基因（2个）和反转录转座子相关基因（9个）。这说明花生属种间杂交人工异源多倍化早期世代发生着快速、剧烈的基因表达变化;从中获得的一些差异基因片段可用于花生属异源多倍化的分子机制研究。

低拷贝核基因在异源多倍体植物中的进化与表达

异源多倍体植物在自然界中广泛分布。在这类植物谱系中,低拷贝核基因具有特殊的进化特点和丰富的植物系统发生信息,在转录水平存在基因沉默、基因激活和不均等表达等特点。以低拷贝核基因为主线,概述了其在多倍体植物系统发生中的应用和相关注意事项,并对其在多倍体植物中的表达变化及其分子机制进行了探讨,系统地介绍了国际上相关领域的研究成果和最新动向。

植物异源多倍体进化中基因表达的变化

多倍化是植物物种进化的主要动力,异源多倍体植物在形成早期发生着快速的基因表达变化。本文概述了异源多倍体植物中基因表达变化的特点,包括基因的沉默、激活和部分同源基因表达水平的变化,探讨了基因表达变化的分子机制和生物学意义,并对研究中的问题进行了分析和展望。

远缘杂交和异源多倍体化技术在水稻育种中的应用

从野生稻遗传资源在育种中的作用出发,概述了栽培稻与野生稻远缘杂交和多倍体化在水稻育种中的应用。对远缘杂交中的杂交不亲和性以及杂种不育等问题采用激素处理、胚挽救等途径解决,对所获杂种从形态学、细胞学、生物化学以及分子生物学等多方面鉴定,对栽野杂种存在的野生性状通过选择与改造相结合的方法而淘汰,对其有利基因则加以选择和聚合以获得稳定优良品种。这些从理论上和实践上证明远缘杂交和多倍体化相结合的异源多倍体化是获得高产优质水稻新品种的一条新途径。

节节麦-黑麦双二倍体的染色体C-带分析

通过对节节麦-黑麦双二倍体及其亲本节节麦、黑麦的C-分带研究,表明节节麦-黑麦双二倍体含有其双亲完整的染色体组,其C-带带型与亲本的C-带带型基本一致,从细胞学水平上证实了该种质是人工合成的一种新的异源多倍体。

对人工合成小麦的微卫星变异分析

比较分析了同一四倍体小麦Langdon与5个不同粗山羊草在合成六倍体小麦前后A、B、D染色体组不同染色体上的微卫星变异,旨在通过分析异源多倍化引起的微卫星位点和序列变异以期探讨异源多倍体的进化机制。在所检测的位于A、B染色体组上各125个特异微卫星(G-SSR)标记中,分别有5个(4.0%)和6个(4.8%)位点发生变异;而在76个A/B染色体组上的表达序列标签微卫星(EST-SSR)标记中,只有2个(2.6%)发生了变异,比A、B染色体组G-SSR变异频率小,说明功能基因区的变异小于重复序列非编码区。在D染色体组上的103个G-SSR标记中,3个位点(2.9%)发生了序列变化。对表现差异的微卫星位点序列分析发现,人工合成小麦中多倍化引起的微卫星序列变异主要表现为简单序列重复单元次数的增加或减少;发生消除的微卫星序列比普通的微卫星序列更易发生不同类型的序列改变。微卫星序列在异源多倍化过程中对新物种基因组的形成可能起到重要的调节作用。