Delineation by fluorescence in situ hybridization of a single hemizygous chromosomal region associated with aposporous embryo sac formation in Pennisetum squamulatum and Cenchrus ciliaris

Apomixis is a means of asexual reproduction by which plants produce embryos without meiosis and fertilization; thus the embryo is of clonal, maternal origin. We previously reported molecular markers showing no recombination with the trait for aposporous embryo sac development in Pennisetum squamulatum and Cenchrus ciliaris, and the collective single-dose alleles defined an apospory-specific genomic region (ASGR). Fluorescence in situ hybridization (FISH) was used to confirm that the ASGR is a hemizygous genomic region and to determine its chromosomal position with respect to rDNA loci and centromere repeats. We also documented chromosome transmission from P. squamulatum in several backcrosses (BCs) with P. glaucum using genomic in situ hybridization (GISH). One to three complete P. squamulatum chromosomes were detected in BC(6), but only one of the three hybridized with the ASGR-linked markers. In P. squamulatum and in all BCs examined, the apospory-linked markers were located in the distal region of the short arm of a single chromosome. All alien chromosomes behaved as univalents during meiosis and segregated randomly in BC(3) and later BC generations, but presence of the ASGR-carrier chromosome alone was sufficient to confer apospory. FISH results support our hypotheses that hemizygosity, proximity to centromeric sequences, and chromosome structure may all play a role in low recombination in the ASGR.     

High-resolution physical mapping reveals that the apospory-specific genomic region (ASGR) in Cenchrus ciliaris is located on a heterochromatic and hemizygous region of a single chromosome

An apomictic mode of reproduction known as apospory is displayed by most buffelgrass (Cenchrus ciliaris) genotypes, but rare sexual individuals have been identified. Previously, intraspecific crosses between sexual and aposporous genotypes allowed linkage to be discovered between the aposporous mode of reproduction and nine molecular markers that had been isolated from an aposporous relative, Pennisetum squamulatum. This region was described as the apospory-specific genomic region (ASGR). We now show an ideogram of the chromosome complement for aposporous tetraploid buffelgrass accession B-12-9 including the ASGR-carrier chromosome. The ASGR-carrier chromosome has a region of hemizygosity, as determined by in situ hybridization of BAC clones and unique morphological characteristics when compared with other chromosomes in the genome. In spite of its unique morphology, the ASGR-carrier chromosome could be identified as one of the chromosomes of a meiosis I quadrivalent. A similar partially hemizygous segment was also detected in the ASGR-carrier chromosome of the aposporous buffelgrass genotype, Higgins, but not in the sexual accession B-2S. Two non-recombining BACs linked to apospory were physically mapped on a highly condensed chromatin region of the short arm of B-12-9, and the distance between the BACs was estimated to be ∼11 Mbp, a distance similar to what previously has been shown in P. squamulatum. The short arm of the ASGR-carrier chromosome was highly condensed at pachytene and extended only 1.7–2.7 fold that of mitotic chromosomes. Low recombination in the ASGR may partially be due to its localization in heterochromatin.     

Recombination within the apospory specific genomic region leads to the uncoupling of apomixis components in Cenchrus ciliaris

Apomixis enables the clonal propagation of maternal genotypes through seed. If apomixis could be harnessed via genetic engineering or introgression, it would have a major economic impact for agricultural crops. In the grass species Pennisetum squamulatum and Cenchrus ciliaris (syn. P. ciliare), apomixis is controlled by a single dominant “locus”, the apospory-specific genomic region (ASGR). For P. squamulatum, 18 published sequenced characterized amplified region (SCAR) markers have been identified which always co-segregate with apospory. Six of these markers are conserved SCARs in the closely related species, C. ciliaris and co-segregate with the trait. A screen of progeny from a cross of sexual × apomictic C. ciliaris genotypes identified a plant, A8, retaining two of the six ASGR-linked SCAR markers. Additional and newly identified ASGR-linked markers were generated to help identify the extent of recombination within the ASGR. Based on analysis of missing markers, the A8 recombinant plant has lost a significant portion of the ASGR but continues to form aposporous embryo sacs. Seedlings produced from aposporous embryo sacs are 6× in ploidy level and hence the A8 recombinant does not express parthenogenesis. The recombinant A8 plant represents a step forward in reducing the complexity of the ASGR locus to determine the factor(s) required for aposporous embryo sac formation and documents the separation of expression of the two components of apomixis in C. ciliaris.     

A segment of the apospory-specific genomic region is highly microsyntenic not only between the apomicts Pennisetum squamulatum and buffelgrass, but also with a rice chromosome 11 centromeric-proximal genomic region

Bacterial artificial chromosome (BAC) clones from apomicts Pennisetum squamulatum and buffelgrass (Cenchrus ciliaris), isolated with the apospory-specific genomic region (ASGR) marker ugt197, were assembled into contigs that were extended by chromosome walking. Gene-like sequences from contigs were identified by shotgun sequencing and BLAST searches, and used to isolate orthologous rice contigs. Additional gene-like sequences in the apomicts' contigs were identified by bioinformatics using fully sequenced BACs from orthologous rice contigs as templates, as well as by interspecies, whole-contig cross-hybridizations. Hierarchical contig orthology was rapidly assessed by constructing detailed long-range contig molecular maps showing the distribution of gene-like sequences and markers, and searching for microsyntenic patterns of sequence identity and spatial distribution within and across species contigs. We found microsynteny between P. squamulatum and buffelgrass contigs. Importantly, this approach also enabled us to isolate from within the rice (Oryza sativa) genome contig Rice A, which shows the highest microsynteny and is most orthologous to the ugt197-containing C1C buffelgrass contig. Contig Rice A belongs to the rice genome database contig 77 (according to the current September 12, 2003, rice fingerprint contig build) that maps proximal to the chromosome 11 centromere, a feature that interestingly correlates with the mapping of ASGR-linked BACs proximal to the centromere or centromere-like sequences. Thus, relatedness between these two orthologous contigs is supported both by their molecular microstructure and by their centromeric-proximal location. Our discoveries promote the use of a microsynteny-based positional-cloning approach using the rice genome as a template to aid in constructing the ASGR toward the isolation of genes underlying apospory.     

High-resolution physical mapping in Pennisetum squamulatum reveals extensive chromosomal heteromorphism of the genomic region associated with apomixis

Gametophytic apomixis is asexual reproduction as a consequence of parthenogenetic development of a chromosomally unreduced egg. The trait leads to the production of embryos with a maternal genotype, i.e. progeny are clones of the maternal plant. The application of the trait in agriculture could be a tremendous tool for crop improvement through conventional and nonconventional breeding methods. Unfortunately, there are no major crops that reproduce by apomixis, and interspecific hybridization with wild relatives has not yet resulted in commercially viable germplasm. Pennisetum squamulatum is an aposporous apomict from which the gene(s) for apomixis has been transferred to sexual pearl millet by backcrossing. Twelve molecular markers that are linked with apomixis coexist in a tight linkage block called the apospory-specific genomic region (ASGR), and several of these markers have been shown to be hemizygous in the polyploid genome of P. squamulatum. High resolution genetic mapping of these markers has not been possible because of low recombination in this region of the genome. We now show the physical arrangement of bacterial artificial chromosomes containing apomixis-linked molecular markers by high resolution fluorescence in situ hybridization on pachytene chromosomes. The size of the ASGR, currently defined as the entire hemizygous region that hybridizes with apomixis-linked bacterial artificial chromosomes, was estimated on pachytene and mitotic chromosomes to be approximately 50 Mbp (a quarter of the chromosome). The ASGR includes highly repetitive sequences from an Opie-2-like retrotransposon family that are particularly abundant in this region of the genome.     

Pennisetum squamulatum: is the predominant cytotype hexaploid or octaploid?

Apomixis is a mode of asexual reproduction where maternal clones are produced through seeds. Consequently, genetic segregation is prevented in hybrid progenies. Pennisetum squamulatum has been used to transfer apomixis into the related sexual species Pennisetum glaucum by the introgression of an apospory-specific genomic region (ASGR)-carrier chromosome. Crosses between P. glaucum and P. squamulatum or Pennisetum purpureum have been relatively easy to make even though P. squamulatum has been reported to have a different basic chromosome number than the other 2 species (9 vs. 7) and to be hexaploid (2n = 6x = 54). Our extensive examination of one accession had shown a chromosome number of 2n = 56. In order to determine if there was a variation among accessions, we counted the number of chromosomes in 5 accessions of P. squamulatum using centromeric and 18S-5.8S-26S rDNA probes as molecular cytological markers. Our results showed that P. squamulatum is most likely octaploid with a basic chromosome number of 7 (2n = 8x = 56) and may belong to the secondary gene pool of Pennisetum. Moreover, a morphologically similar ASGR-carrier chromosome that confers apomixis was observed in all accessions.     

Chromosomes carrying meiotic avoidance loci in three apomictic eudicot Hieracium subgenus Pilosella species share structural features with two monocot apomicts

The LOSS OF APOMEIOSIS (LOA) locus is one of two dominant loci known to control apomixis in the eudicot Hieracium praealtum. LOA stimulates the differentiation of somatic aposporous initial cells after the initiation of meiosis in ovules. Aposporous initial cells undergo nuclear proliferation close to sexual megaspores, forming unreduced aposporous embryo sacs, and the sexual program ceases. LOA-linked genetic markers were used to isolate 1.2 Mb of LOA-associated DNAs from H. praealtum. Physical mapping defined the genomic region essential for LOA function between two markers, flanking 400 kb of identified sequence and central unknown sequences. Cytogenetic and sequence analyses revealed that the LOA locus is located on a single chromosome near the tip of the long arm and surrounded by extensive, abundant complex repeat and transposon sequences. Chromosomal features and LOA-linked markers are conserved in aposporous Hieracium caespitosum and Hieracium piloselloides but absent in sexual Hieracium pilosella. Their absence in apomictic Hieracium aurantiacum suggests that meiotic avoidance may have evolved independently in aposporous subgenus Pilosella species. The structure of the hemizygous chromosomal region containing the LOA locus in the three Hieracium subgenus Pilosella species resembles that of the hemizygous apospory-specific genomic regions in monocot Pennisetum squamulatum and Cenchrus ciliaris. Analyses of partial DNA sequences at these loci show no obvious conservation, indicating that they are unlikely to share a common ancestral origin. This suggests convergent evolution of repeat-rich hemizygous chromosomal regions containing apospory loci in these monocot and eudicot species, which may be required for the function and maintenance of the trait.     

Sequence analysis of bacterial artificial chromosome clones from the apospory-specific genomic region of Pennisetum and Cenchrus

Apomixis, asexual reproduction through seed, is widespread among angiosperm families. Gametophytic apomixis in Pennisetum squamulatum and Cenchrus ciliaris is controlled by the apospory-specific genomic region (ASGR), which is highly conserved and macrosyntenic between these species. Thirty-two ASGR bacterial artificial chromosomes (BACs) isolated from both species and one ASGR-recombining BAC from P. squamulatum, which together cover approximately 2.7 Mb of DNA, were used to investigate the genomic structure of this region. Phrap assembly of 4,521 high-quality reads generated 1,341 contiguous sequences (contigs; 730 from the ASGR and 30 from the ASGR-recombining BAC in P. squamulatum, plus 580 from the C. ciliaris ASGR). Contigs containing putative protein-coding regions unrelated to transposable elements were identified based on protein similarity after Basic Local Alignment Search Tool X analysis. These putative coding regions were further analyzed in silico with reference to the rice (Oryza sativa) and sorghum (Sorghum bicolor) genomes using the resources at Gramene (www.gramene.org) and Phytozome (www.phytozome.net) and by hybridization against sorghum BAC filters. The ASGR sequences reveal that the ASGR (1) contains both gene-rich and gene-poor segments, (2) contains several genes that may play a role in apomictic development, (3) has many classes of transposable elements, and (4) does not exhibit large-scale synteny with either rice or sorghum genomes but does contain multiple regions of microsynteny with these species.     

Targeted sequencing of a complex locus within a polyploid genome using reduced representation libraries

Apospory is a form of gametophytic apomixis in which embryos develop from unreduced embryo sacs derived from aposporous initials formed from nucellar cells of ovules to produce offspring genetically identical to the female plant. Apospory in Pennisetum squamulatum (8X) and Cenchrus ciliaris (4X) is a dominant trait controlled by a physically large, hemizygous, heterochromatic chromosomal block called the apospory-specific genomic region (ASGR). Both apomictic species are polyploid, with genome sizes estimated at 2600 to 3000 Mbp for C. ciliaris and 9400 to 10,300 Mbp for P. squamulatum. A study was conducted to determine whether duplex-specific nuclease (DSN) normalization of DNA from apomictic and sexual genotypes would reduce repetitive sequences and allow bioinformatic analysis to predict sequence contigs derived from the ASGR. DSN libraries from four genotypes were sequenced using Illumina^® HiSeq 2000 technology. 39 out of 44 tested sequence characterized amplified region (SCAR) markers from in silico predicted ASGR-specific contigs were mapped to the ASGR in a Pennisetum F₁ mapping population. Eighteen SCARs showed apomict-specific amplification in C. ciliaris. The successful mapping of ~90 % of the SCAR markers to the ASGR in the Pennisetum F₁ mapping population shows that DSN normalization and Illumina sequencing can be used as an effective strategy for targeted mapping of a physically large locus rich in repetitive sequences, like that of the ASGR.     

Embryological Studies on Apomixis in Pennisetum squamulatum

Studies on the formation and development of the embryo sac of the apomictic material of Pennisetum squamulatum Fresen indicated that normal archesporial cell did form with consequent development of a megaspore mother cell and later meiotic division to give rise to a triad. But invariably the megaspore mother cell and the triad underwent degeneration after formation. During the period of formation or degeneration of the megaspore or the triad a number of nucellar cells around the degenerated sexual cell became much enlarged. Frequently, one of the enlarging nucellar cells near the micropylar end became vacuolated and then developed into an aposporous uninucleate embryo sac, which underwent two further mitotic divisions to form an aposporous four-nucleate embryo sac, where the four nuclei remained in the micropylar end. Thus in the mature aposporous embryo sac there were one egg cell, one synergid and one central cell (containing two polar nuclei). Antipodal cells were completely lacking. The pattern of development of the aposporous embryo sac resembles the panicum type. There were two types of embryo formed during apomictic development namely ( 1 ) The pre-genesis embryo--embryo formed without fertilization, 1 to 2 days before anthesis, and (2) The late-genesis embryo--derived from the unfertilized egg cells, 3 to 4 days after anthesis. In the late-genesis embryo type, the egg cell divided after the secondary nucleus has undergone division to form the endosperm nuclei. All egg cells developed vacuoles before they differentiated into embryos. The development of the aposporous embryo followed the sequence of the formation of globular, pearshaped embryo and full stages of differentiation. The unfertilized secondary nucleus divides to form free endosperm nuclei after being stimulated by pollination. The development of the endosperm belongs to the nuclear-type.     

Is supernumerary chromatin involved in gametophytic apomixis of polyploid plants?

Gametophytic apomixis, or unreduced embryo sac development that results in asexual reproduction through seeds, occurs in several families of angiosperms and must be polyphyletic in origin. The molecular mechanisms underlying gametophytic apomixis have not been discovered and are the subject of intense investigation. A common feature of almost all apomicts is their polyploid nature. From genetic mapping studies in both monocots and dicots, there is low genetic recombination associated with a single (rarely two), dominant locus for either aposporous or diplosporous embryo sac formation. In Pennisetum squamulatum and Cenchrus ciliaris, some DNA sequences mapping to the apospory locus are unique to apomictic genotypes and apparently hemizygous. This sequence divergence at the apomixis locus could be a consequence of genome rearrangements and isolation from genetic recombination, both of which may have contributed to the definition of a chromosomal region as supernumerary. The possible involvement of supernumerary chromatin, formed as a result of interspecific hybridization, in the origin of apomixis, is explored here. Received: 26 October 2000 / Revision accepted: 5 April 2001     

非洲狼尾草未受精无孢子生殖胚囊退化研究

为理解植物无孢子生殖胚囊未受精条件下的退化,对无孢子生殖植物非洲狼尾草未受精成熟胚囊中央细胞退化做了细胞形态学研究。没有受精的中央细胞退化时最显著的特点是细胞核产生核膜囊泡。核膜囊泡有两种类型:单层膜的囊泡和双层膜的囊泡,单层膜囊泡在细胞质中,双层膜囊泡在细胞核内。核膜囊泡有两种发生方式:1)核膜的外膜向细胞质一侧膨胀产生囊泡,囊泡进入细胞质;2)核膜向核内凹陷形成囊泡,囊泡进入细胞核。核膜囊泡类型与产生方式密切关联。核膜囊泡吞噬并消化包括线粒体在内的细胞质和核质。     

Study on Degeneration of Unfertilized Aposporous Embryo Sac in Pennisetum squamulatium (Gramineae)

To understand the degeneration of unfertilized aposporous embryo sac in an aposporous species Pennisetum squamulatum, the central cell in the unfertilized embryo sac was characterized ultrastructurally . The most prominent sign of degeneration is that the central cell nucleus produced nuclear vacuoles . These nuclear vacuoles can be classified into singleanddouble- layered types . Single- layered nuclear vacuoles are found in the cytoplasm, while the double-layered are inside the nucleus . There are two ways to produce nuclear vacuoles . One is that the outer membrane of the nuclear envelope distends towards the cytoplasm to form nuclear vacuoles ; and the other is the double-layered nuclear envelope derives vacuoles by depressing inwards . Nuclear envelope types are in relation to the ways they are produced . All nuclear vacuoles absorb cytoplasm or nuclear matrix , and trap organelles such as mitochondria .     

水蔗草兼性无融合生殖胚胎学研究

对水蔗草 (ApludamuticaL .)的生殖方式进行研究 ,结果表明水蔗草进行兼性无融合生殖。胚囊发育分为两种类型 ,即有性生殖的蓼型和无孢子生殖的大黍型。无融合生殖胚囊频率为 6 0 .74%。在大孢子母细胞发育至四分体后 ,珠孔端的 3个大孢子解体。合点端的大孢子未解体时 ,邻近大孢子的 1个珠心细胞开始特化 ,形成无融合生殖的原始细胞 ,由该原始细胞发育形成有 1个卵细胞、1个助细胞和 2个极核的四核胚囊。     

水蔗草兼性无融合生殖胚胎学研究

对水蔗草(Apluda mutica L.)的生殖方式进行研究,结果表明水蔗草进行兼性无融合生殖.胚囊发育分为两种类型,即有性生殖的蓼型和无孢子生殖的大黍型.无融合生殖胚囊频率为60.74%.在大孢子母细胞发育至四分体后,珠孔端的3个大孢子解体.合点端的大孢子未解体时,邻近大孢子的1个珠心细胞开始特化,形成无融合生殖的原始细胞,由该原始细胞发育形成有1个卵细胞、1个助细胞和2个极核的四核胚囊.     

Identification and physical localization of useful genes and markers to a major gene-rich region on wheat group 1S chromosomes

The short arm of Triticeae homeologous group 1 chromosomes is known to contain many agronomically important genes. The objectives of this study were to physically localize gene-containing regions of the group 1 short arm, enrich these regions with markers, and study the distribution of genes and recombination. We focused on the major gene-rich region ("1S0.8 region") and identified 75 useful genes along with 93 RFLP markers by comparing 35 different maps of Poaceae species. The RFLP markers were tested by gel blot DNA analysis of wheat group 1 nullisomic-tetrasomic lines, ditelosomic lines, and four single-break deletion lines for chromosome arm 1BS. Seventy-three of the 93 markers mapped to group 1 and detected 91 loci on chromosome 1B. Fifty-one of these markers mapped to two major gene-rich regions physically encompassing 14% of the short arm. Forty-one marker loci mapped to the 1S0.8 region and 10 to 1S0.5 region. Two cDNA markers mapped in the centromeric region and the remaining 24 loci were on the long arm. About 82% of short arm recombination was observed in the 1S0.8 region and 17% in the 1S0.5 region. Less than 1% recombination was observed for the remaining 85% of the physical arm length.     

水蔗草胚珠附器的研究

本文对水蔗草的胚珠附器进行研究,结果表明：在功能大孢子时期,珠孔端的1～3个珠心细胞开始特化,发育成胚珠附器;胚珠附器发生时,有些胚珠同时出现无孢子生殖原始细 胞;有性生殖和无孢子生殖的胚囊中均有胚珠附器存在;但在无孢子生殖的胚囊中,胚珠附器一般很大,长约是宽的1～３倍;而有性生殖胚囊的胚珠附器的长约是宽的1～２倍;和有性生殖胚囊相比,无孢子生殖胚囊的胚珠附器更加发达;存在发达的胚珠附器是水蔗草无孢子生殖胚囊的特点之一。