Origin and evolution of a new tetraploid mangrove species in an intertidal zone

Polyploidy is a major factor in the evolution of plants,yet we know little about the origin and evolution of polyploidy in intertidal species.This study aimed to identify the evolutionary transitions in three truemangrove species of the genus Acanthus distributed in the Indo-West Pacific region.For this purpose,we took an integrative approach that combined data on morphology,cytology,climatic niche,phylogeny,and biogeography of 493 samples from 42 geographic sites.Our results show that the Acanthus ilicifolius lineage distributed east of the Thai-Malay Peninsula possesses a tetraploid karyotype,which is morphologically distinct from that of the lineage on the west side.The haplotype networks and phylogenetic trees for the chloroplast genome and eight nuclear genes reveal that the tetraploid species has two sub-genomes,one each from A.ilicifolius and A.ebracteatus,the paternal and maternal parents,respectively.Population structure analysis also supports the hybrid speciation history of the new tetraploid species.The two sub-genomes of the tetraploid species diverged from their diploid progenitors during the Pleistocene.Environmental niche models revealed that the tetraploid species not only occupied the near-entire niche space of the diploids,but also expanded into novel environments.Our findings suggest that A.ilicifolius species distributed on the east side of the Thai-Malay Peninsula should be regarded as a new species,A.tetraploideus,which originated from hybridization between A.ilicifolius and A.ebracteatus,followed by chromosome doubling.This is the first report of a true-mangrove allopolyploid species that can reproduce sexually and clonally reproduction,which explains the long-term adaptive potential of the species.

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.

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.

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.

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.

A comparative analysis of small RNAs between two Upland cotton backcross inbred lines with different fiber length: Expression and distribution

The cotton fiber is the most important raw material for the textile industry and an ideal model system for studying cell elongation. However, the genetic variation of fiber elongation in relation to miRNA is poorly understood. A high-throughput comparative RNA-seq of two lines differing in fiber length(FL) from a backcross inbred line(BIL)population of G. hirsutum × G. barbadense revealed differentially expressed(DE) miRNAs and their targets in rapidly elongating fibers. A real-time quantitative PCR analysis was further performed to validate the results. A total of 463(including 47 DE) miRNAs were identified,and seven DE miRNAs were co-localized with seven FL quantitative trait loci(QTL)identified in the G. hirsutum × G. barbadense population. Of 82(including 21 DE) targets identified, nine(including one DE) were also co-localized with the seven FL QTL. The relationship between the allopolyploid and its diploid ancestral species with respect to miRNAs and their targets was also characterized. These results will facilitate the understanding of the molecular genetic mechanism of fiber elongation with regards to miRNAs in cotton.

A catalog of gliadin alleles:Polymorphism of 20th-century common wheat germplasm

A new, improved version of the catalog of 182 alleles at the six Gli loci of common wheat(T.aestivum L.) shown in electrophoregrams of 128 standard genotypes was used for analysis of1060 cultivars and lines bred in the 20 th century. The most frequent alleles in the studied germplasm occurred with frequencies of 18%–40%, with 30 unique alleles, one in each cultivar. Extremely high genetic diversity was found(average H for the six main Gli loci was0.870 ± 0.046), nearly identical in winter(H = 0.831) and spring(H = 0.856) wheats but differing among 28 groups of cultivars released in 22 countries. Each country or region was characterized by its own specific set of the most frequent Gli alleles, and the 28 cultivar groups formed five main relationship clusters if polymorphism at the six Gli loci was considered. However, different levels of similarity between groups of cultivars were found if polymorphism of the A, B, or D genomes of common wheat was tested separately. In general, the 20 th century germplasm of common wheat was differentiated and structured by country or region and cultivar type(spring or winter). Each elemental genome(in particular, A and D) contributed to the structure of the polymorphism studied. We propose that the structure of the wheat germplasm was a result of natural selection under the ecoclimatic conditions of cultivation specific to each country or region. As many as 27.4% of cultivars studied violated the requirement of the DUS rules for uniformity, being represented by mixtures of two or more closely related genotypes. However, the composition of a cultivar as a set of related but different genotypes may contribute to its adaptivity, and thereby to the known high plasticity of common wheat.

Dosage effect genes modulate grain development in synthesized Triticum durum-Haynaldia villosa allohexaploid

Polyploidization in plants often leads to increased cell size and grain size,which may be affected by the increased genome dosage and transcription abundance.The synthesized Triticum durum(AABB)-Hay-naldia villosa(WM)amphiploid(AABBM)has significantly increased grain size,especially grain length,than the tetraploid and diploid parents.To investigate how polyploidization affects grain development at the transcriptional level,we perform transcriptome analysis using the immature seeds of T.durum,H.villosa,and the amphiploid.The dosage effect genes are contributed more by differentially expressed genes from genome V of H.villosa.The dosage effect genes overrepresent grain development-related genes.Inter-estingly,the vernalization gene TaVRN1 is among the positive dosage effect genes in the T.durum-H.villosa and T.turgidum-Ae.tauschii amphiploids.The expression levels of TaVRN1 homologs are positively correlated with the grain size and weight.The TaVRN1-B1 or TaVRN1-D1 mutation shows delayed florescence,decreased cell size,grain size,and grain yield.These data indicate that dosage effect genes could be one of the important explanations for increased grain size by regulating grain development.The identification and functional validation of dosage effect genes may facilitate the finding of valuable genes for improvingwheat yield.

一种独特的无减数融合生殖方式的发现及一条合成不育异源多倍体高效路径的创建

多倍化与生殖方式转换之间的联系作为进化遗传学的热点,能被开拓为农业生物遗传改良的新路径.最近我们通过整合雌核生殖银鲫和有性生殖鲫的基因组,创制了一个新双三倍体群体,发现它们中的大部分雌性恢复了单性雌核生殖能力.在本研究中,我们发现少数雌性获得了一种定义为“无减数融合生殖”的独特生殖方式.具有这种生殖方式的新双三倍体雌性不仅从单性雌核生殖银鲫遗传了无减数分裂产生不减数卵子的能力,还从有性生殖鲫遗传了卵核与精核融合形成受精卵的能力.随后我们将这种新双三倍体与二倍体团头鲂进行交配,直接创制了一个合成异源七倍体群体.它们的染色体组由来自其母本新双三倍体鲫的全套染色体组和来自父本二倍体团头鲂的一套染色体组构成.此外,我们还在一尾异源七倍体的部分体细胞中,检测到鲫与团头鲂染色体间相互易位的现象.随后我们追踪了异源七倍体生殖细胞在减数分裂过程中的染色体行为,揭示了它们不育的细胞学机制.结果表明,在减数第一次分裂(减Ⅰ)前期,染色体联会异常以及DNA双链断裂无法被完全修复,导致异源七倍体初级卵母细胞严重凋亡.尽管其初级精母细胞在减Ⅰ前期表现出与初级卵母细胞相似的染色体行为,但它们可以发育到减Ⅰ中期,并最终由于同源染色体分离失败而发生凋亡.最后,我们建立了一个可持续大规模生产具有无减数融合生殖能力的新双三倍体克隆系,还将其与多种鲤科鱼类进行交配快速创制出多种整合有不同鲤科鱼类基因组的不育异源多倍体群体,由此研发出一条高效的育种技术路径.本研究不仅拓宽了我们对脊椎动物生殖方式转换的认识,还为多倍体育种和杂种优势固定提供了一个可行的策略.

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.

Natural and artificial polyploids in aquaculture

Genome polyploidy has been revealed to result in evolutionary advantages and novelties,and therefore,polyploid aquatic animals may possess excellent traits of economic interest including rapid growth,extensive adaptability and disease resistance.For this reason,numerous species of natural polyploid fishes,such as common carp,gibel carp,crucian carp,salmon,and sturgeon,were chosen as important target species for aquaculture.Many artificial polyploids have been commercially utilized for aquaculture and most of them were created from natural polyploid fishes of the Cyprinidae and Salmonidae.Thanks to the easy mass production and better economic traits in growth and flesh quality,the synthetized autopolyploids or allopolyploids from natural polyploid species in cyprinid fishes have been extensively applied to aquaculture throughout China.This review outlines polyploidy advantages and innovative opportunities,lists natural polyploid species used in aquaculture,and summarizes artificial polyploids that have been induced or synthetized,and used in aquaculture.Moreover,some main research trends on polyploid utilization and ploidy manipulation of aquaculture animals are also introduced and discussed in the review.

Two unisexual artificial polyploid clones constructed by ge-nome addition of common carp(Cyprinus carp)and crucian carp(Carassius auratus)

A polyploid hybrid fish with natural gynogenesis can prevent segregation and maintain their hybrid vigor in their progenies. Supposing the reproduction mode of induced polyploid fish being natural gynogenesis, allopolyploid hybrid between common carp and crucian carp into allo-polyploid was performed. The purpose of this paper is to describe a lineage from sexual diploid carp transforming into allotriploid and allotetraploid unisexual clones by genome addition. The dip-loid hybrid between common carp and crucian carp reproduces an unreduced nucleus consisting of two parental genomes. This unreduced female pronucleus will fuse with male pronucleus and form allotriploid zygote after penetration of related species sperms. Allotriploid embryos grow nor-mally, and part of female allotriploid can produce unreduced mature ova with three genomes. Ma-ture ova of most allotriploid females are provided with natural gynogenetic trait and their nuclei do not fuse with any entrance sperm. All female offspring are produced by gynogenesis of allotriploid egg under activation of penetrating sperms. These offspring maintain morphological traits of their allotriploid maternal and form an allotetraploid unisexual clone by gynogenetic reproduction mode. However, female nuclei of rare allotriploid female can fuse with penetrating male pronuclei and result in the appearance of allotetraploid individuals by means of genome addition. All al-lotetraploid females can reproduce unreduced mature eggs containing four genomes. Therefore, mature eggs of allotetraploid maintain gynogenetic trait and allotetraploid unisexual clone is pro-duced under activation of related species sperms.

Synthesizing double haploid hexaploid wheat populations based on a spontaneous alloploidization process

Doubled haploid （DH） populations are useful to scientists and breeders in both crop improvement and basic research. Current methods of producing DHs usually need in vitro culture for extracting haploids and chemical treatment for chromosome doubling. This report describes a simple method for synthesizing DHs （SynDH） especially for allopolyploid species by utilizing meiotic restitution genes. The method involves three steps： hybridization to induce recombination, interspecific hybridization to extract haploids, and spontaneous chromosome doubling by selfing the interspecific Fis. DHs produced in this way contain recombinant chromosomes in the genome（s） of interest in a homogeneous background. No special equipment or treatments are involved in the DH production and it can be easily applied in any breeding and/or genetic program. Triticum turgidum L. and Aegilops tauschii Coss, the two ancestral species of common wheat （Triticurn aestivum L.） and molecular markers were used to demonstrate the SynDH method.

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.

Effect of Whole-Genome Duplication on the Evolutionary Rescue of Sterile Hybrid Monkeyflowers

Hybridization is a creative evolutionary force,increasing genomic diversity and facilitating adaptation and even speciation.Hybrids often face significant challenges to establishment,including reduced fertility that arises from genomic incompatibilities between their parents.Whole-genome duplication in hybrids(allopolyploidy)can restore fertility,cause immediate phenotypic changes,and generate reproductive isolation.Yet the survival of polyploid lineages is uncertain,and few studies have compared the performance of recently formed allopolyploids and their parents under field conditions.Here,we use natural and synthetically produced hybrid and polyploid monkeyflowers(Mimulus spp.)to study how polyploidy contributes to the fertility,reproductive isolation,phenotype,and performance of hybrids in the field.We find that polyploidization restores fertility and that allopolyploids are reproductively isolated from their parents.The phenotype of allopolyploids displays the classic gigas effect of whole-genome duplication,in which plants have larger organs and are slower to flower.Field experiments indicate that survival of synthetic hybrids before and after polyploidization is intermediate between that of the parents,whereas natural hybrids have higher survival than all other taxa.We conclude that hybridization and polyploidy can act as sources of genomic novelty,but adaptive evolution is key in mediating the establishment of young allopolyploid lineages.

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.

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