Haploids can be induced in knockout mutants of OsPLA1,but not OsDMP3 or OsDMP6,in rice

Doubled haploid(DH)technology is an important tool in crop breeding because it can significantly accelerate the breeding process.ZmPLA1/MATL/NLD and ZmDMP are two key genes controlling haploid induction(HI)in maize,exhibiting a synergistic effect.However,it is unknown whether knock out of ZmDMP orthologs can stimulate HI in rice.In this study,a ZmPLA1 ortholog(OsPLA1)and two ZmDMP orthologs(OsDMP3 and OsDMP6)were identified in rice.All three genes encode plasma membrane-localized proteins and were highly expressed in mature anthers.Knockout of OsPLA1 in both Minghui 63 and Nipponbare resulted in reduced seed setting rate(SSR)and caused HI.The osdmp3,osdmp6 and the double mutant failed to trigger HI independently,nor increased the haploid induction rate(HIR)when combined with ospla1.Repeated pollinations operations of QX654A with the ospla1 mutant significantly improve SSR,while reducing HIR.RNA-seq profiling of mature ospla1 mutant anthers indicated that a large number of differentially expressed genes(DEGs)were enriched in redox homeostasis and lipid metabolic GO terms,plant hormone signal transduction,and MAPK signaling pathways.These findings provide important insights towards construction of an efficient DH breeding technology and study of the molecular mechanism of HI in rice.

Cytological Observation of Pollen Abortion of Lycium barbarum Haploids from Anther Culture

To reveal the sterility characteristics of Lycium barbarum haploids, cytological observations were made on the anthers of Ningqi No.1 and its haploids obtained from anther culture. The results showed that there were no significant differences in anther development between Ningqi No.1 and its haploids at the stage of pollen mother cell, and tetrads were formed successfully after the meiosis stage. The tetrads of Ningqi No.1 could release microspores. At the same time, the tapetal cells can provide nutrition for the development of the microspores, which eventually developed into mature pollen grains. Although the haploids could also release microspores at the tetrad stage, the tapetal cells degraded in advance, which made the released microspores unable to develop into mature pollen grains, resulting in pollen abortion of haploids.

Regenerating Plants from Cryopreserved Adventitious Buds of Haploids in Rice

０ＩｎｔｒｏｄｕｃｔｉｏｎＴｈｅｄｅｖｅｌｏｐｍｅｎｔｏｆｃｒｙｏｐｒｅｓｅｒｖａｔｉｏｎｈａｓｏｆ－ｆｅｒｅｄａｎｅｗｗａｙｏｆｌｏｎｇ－ｔｅｒｍｐｒｅｓｅｒｖａｔｉｏｎｏｆｐｌａｎｔｇｅｒｍｐｌａｓｍｓ．ＳｉｎｃｅＮａｇａｎｄＳｔｒｅｅｔ（１９７...

Elite,transformable haploid inducers in maize

The introduction of alleles into commercial crop breeding pipelines is both time consuming and costly.Two technologies that are disrupting traditional breeding processes are doubled haploid(DH)breeding and genome editing(GE).Recently,these techniques were combined into a GE trait delivery system called HI-Edit(Haploid Inducer-Edit).In HI-Edit,the pollen of a haploid inducer line is reprogrammed to deliver GE traits to any variety,obviating recurrent selection.For HI-Edit to operate at scale,an efficient transformable HI line is needed,but most maize varieties are recalcitrant to transformation,and haploid inducers are especially difficult to transform given their aberrant reproductive behaviors.Leveraging marker assisted selection and a three-tiered testing scheme,we report the development of new Iodent and Stiff Stalk maize germplasm that are transformable,have high haploid induction rates,and exhibit a robust,genetically-dominant anthocyanin native trait that may be used for rapid haploid identification.We show that transformation of these elite‘‘HI-Edit”lines is enhanced using the BABYBOOM and WUSCHEL morphogenetic factors.Finally,we evaluate the HI-Edit performance of one of the lines against both Stiff Stalk and non-Stiff Stalk testers.The strategy and results of this study should facilitate the development of commercially scalable HI-Edit systems in diverse crops.

Patterns of DNA cytosine methylation between haploids and corresponding diploids in rice

Eighteen pairs of diploid-haploid twin-seedlings were identified and screened out fromspecial rice SARII-628 population. Five pairs of themwere selected and randomly designated as A, B, C, Dand E. Simple sequence repeats (SSR) analysisshowed that there was no difference among 310 siteswhich indicated that there was no base mutation onDNA primary structure. DNA methylation plays animportant role in gene expression regulation duringgrowth and development stages in eukaryotes. Amodified AFLP technique (methylation-sensitiveAFLP, MSAP) was employed to detect the DNA me-thylation patterns in the 5′-CCGG sites of the fivepairs of twin-seedlings. Although no methylationmutation was detected among the five diploids,forty-three methylation mutation sites were foundfrom the corresponding haploids. The MSAP ratios,which were the ratios of MSAP sites to the total am-plified sites, in five haploids were 18.79%, 19.35%,18.49%, 18.45% and 18.75%, respectively. And cor-responding full methylation levels (5′-CmCGG indouble strands) of those haploids were 10.58%,11.3%, 10.11%, 10.09% and 10.34%, respectively.Both MSAP and full methylation levels in the fivehaploids were higher than that of their correspondingdiploids, which suggested that hypermethylation oc-curred in some 5′-CCGG sites. Five types of MASPpatterns among the five pairs of twin-seedlings weredetected as follows: (1) no changes, methylation lev-els were the same in both haploids and diploids; (2) demethylation, diploid was methylated but no me-thylation in the same site in haploid; (3) hypermethy-lation, the methylation level in haploid was higher than those in diploid; (4) hypomethylation, methyla-tion in haploid was lower than those in diploid; (5) undecided pattern, change trend of methylation lev-els in haploids was not decided. The bands of 18 sites were reclaimed, then sequenced and searched on website to determine the sites of those sequences on rice chromosomes. The result showed that the methylation mutation involved the whole rice genome and 12 pairs of chromosomes. The mutation was site-related and there were different mutation sites for different haploids. Compared to diploids, the higher methylation level in haploids might be a readjusting reaction to the decrease in ploidy for the sake of sur-vival.

The microarray analysis for gene expression in haploids and diploids derived from twin-seedling rice

In this study, microarray technique was employed to analyze the gene expression at the RNA level between haploids and corresponding diploids derived from a rice twin-seedling line SARII-628. Differ- ent degrees of expression variations were observed in the plant after haploidization. The main results are as follows: (1) after haploidization, the ratio of the sensitive loci was 2.47% of the total loci designed on chip. Those loci were randomly distributed on the 12 pairs of rice chromosomes and the activated loci were more than the silenced ones. (2) Gene clusters on chromosome were observed for 33 se- quences. (3) GoPipe function classification for 575 sensitive loci revealed an involvement in the bio- logical process, cell component and molecular function. (4) RT-PCR generally validated the result from microarray with a coincidence rate of 83.78%. And for the randomly-selected activated or silenced loci in chip analysis, the coincidence rate was up to 91.86%.

Exceptionally high genetic variance of the doubled haploid(DH)population of poplar

Doubled haploid(DH)plants have been widely used for breeding and biological research in crops.Pop ulus spp.have been used as model woody plant species for biological research.However,the induction of DH poplar plants is onerous,and limited biological or breeding work has been carried out on DH individuals or populations.In this study,we provide an effective protocol for poplar haploid induction based on an anther culture method.A total of 96 whole DH plant lines were obtained using an F1hybrid of Populus simonii×P.nigra as a donor tree.The phenotypes of the DH population showed exceptionally high variance when compared to those of half-sib progeny of the donor tree.Each DH line displayed distinct features compared to those of the other DH lines or the donor tree.Additionally,some excellent homozygous lines have the potential to be model plants in genetic and breeding studies.

Generation of a human haploid neural stem cell line for genome-wide genetic screening

BACKGROUND Haploid embryonic stem cells(haESCs)have been established in many species.Differentiated haploid cell line types in mammals are lacking due to spontaneous diploidization during differentiation that compromises lineage-specific screens.AIM To derive human haploid neural stem cells(haNSCs)to carry out lineage-specific screens.METHODS Human haNSCs were differentiated from human extended haESCs with the help of Y27632(ROCK signaling pathway inhibitor)and a series of cytokines to reduce diploidization.Neuronal differentiation of haNSCs was performed to examine their neural differentiation potency.Global gene expression analysis was conducted to compare haNSCs with diploid NSCs and haESCs.Fluorescence activated cell sorting was performed to assess the diploidization rate of extended haESCs and haNSCs.Genetic manipulation and screening were utilized to evaluate the significance of human haNSCs as genetic screening tools.RESULTS Human haESCs in extended pluripotent culture medium showed more compact and smaller colonies,a higher efficiency in neural differentiation,a higher cell survival ratio and higher stability in haploidy maintenance.These characteristics effectively facilitated the derivation of human haNSCs.These human haNSCs can be generated by differentiation and maintain haploidy and multipotency to neurons and glia in the long term in vitro.After PiggyBac transfection,there were multiple insertion sites in the human haNSCs’genome,and the insertion sites were evenly spread across all chromosomes.In addition,after the cells were treated with manganese,we were able to generate a list of manganese-induced toxicity genes,demonstrating their utility as genetic screening tools.CONCLUSION This is the first report of a generated human haploid somatic cell line with a complete genome,proliferative ability and neural differentiation potential that provides cell resources for recessive inheritance and drug targeted screening.

Genetics of Fertility Restoration in Cytoplasmic Male Sterile Pepper

Pepper hybrid seeds production using male sterility could lower cost by reducing time and labour, and increase thegenetic purity of the F1 seeds. To investigate the genetics of fertility restoration of the Peterson cytoplasmic sterility inpepper, a doubled haploid population of 115 pepper lines obtained from anther culture of the F1 hybrid between YoloWonder (sterility maintainer line) and Perennial (fertility restorer line) and the parental lines were test-crossed by 77013A(a strict cytoplasmic-genic male sterile line). The fertility of the test-crossed lines was assessed in greenhouse and openfield with the following three criteria: pollen index (PI, visual estimation of pollen amount per flower), pollen number (PN,pollen counting under microscope), and seed number (SN, the number of seeds per fruit in open pollination). Correlationsbetween the each couple of criteria within, as well as between the cultivation methods ranged from 0.55 to 0.84. Analysisof variance showed that the genotype (DH line) and environment were the significant sources of variation of the fertility.Narrow sense of heritance of fertility restoration ranged from 0.38 to 0.92, depending on the criteria and environment. Thedistribution of the progeny was continuous between the parental genotypes indicating the quantitative inheritance offertility restoration. Inferred from segregation according to Snape et al.(1984), the number of segregating genes wasestimated to be that three to four genetic factors were involved in pollen traits (PI and PN) and five to eight genetic factorsin seed production (SN). The heredity analysis of the CMS will be helpful for understanding of the genetic mechanism ofthe fertility restoration and the exploitation of the CMS in hybrid seed production.

Development of high-oil maize haploid inducer with a novel phenotyping strategy

Doubled haploid(DH) technology is important in modern maize breeding. Haploid inducers determine the efficiency of both haploid induction and identification. It has taken decades to improve the efficiency,haploid induction rate(HIR), from the ~2% of the ancestor haploid inducer, stock6, to the ~10% of modern haploid inducers. Improvement of kernel oil content(KOC) would further enhance haploid identification efficiency. Using molecular marker-assisted selection, in combine with the number of haploids per ear as phenotypic criterion, we developed a new high-oil haploid inducer line, CHOI4, with a mean HIR of 15.8%and mean KOC of 11%. High KOC of CHOI4 can achieve a mean accuracy greater than 90% in identification of haploids of different backgrounds, with reduced false discovery rates and false negative rates in comparison with the previous high-oil haploid inducer line, CHOI3. Comparison of phenotypic selection strategies suggested that the number of haploids per ear can be used as a phenotyping criterion during haploid inducer line development. CHOI4 could further increase the efficiency of large-scale DH breeding programs with lower cost.

QTL for grain yield and yield parameters in winter wheat(Triticum aestivum L.)

Field trials with a set of 108 doubled haploid lines(DHs) derived from a cross between the Chinese winter wheat cvs.CA9613 and H1488 were run at Beijing(China).Phenotypic data were recorded for major agronomic yield traits,i.e.grain weight per ear,grain number per ear and thousand grain weight(Tgw) in two field trials at Beijing.Based on the phenotypic data and a genetic map comprising 168 SSR markers,an analysis of quantitative trait loci(QTL) was carried out for yield and yield parameters using the composite interval mapping(CIM) approach.A total of 14 QTL were detected for these traits across two environments.Four of these QTL located on chromosomes 1A and 2B,respectively,exhibited pleiotropic effects.Loci showing pleiotropic effects will be very useful for understanding the homeologous relationships of QTL and designing an appropriate marker-assisted selection programme by multi-trait selection in order to accumulate("pyramide") favorable alleles at different loci.

Developmental Dynamics of Wheat (<i>Triticum aestivum</i>L.) Microspores under Culture

Doubled haploid production via microspore culture is a technique known to accelerate crop breeding by shortening the breeding cycle through achieving homozygosity in one generation. Prior research observed that some embryogenic microspores aborted their development before reaching the embryoid stage. Such embryogenic abortion reduces embryoid yield, making microspore cultures less efficient. The present research aims at identifying stages during which microspore development is susceptible to embryogenic abortion. Information gained through delineation of the developmental dynamics of microspores in culture could be used to improve the efficiency of microspore culture. Embryogenic microspores were isolated from stress-treated wheat (Triticum aestivum L.) tillers and cultured in liquid medium. The development of embryogenic microspores was monitored over a 35 day period. At day 7, 10, 14, 21, 28, and 35, the developing microspores were counted and categorized into multicellular structures, pre-embryoids, immature embryoids and mature embryoids. The results showed that 44% - 62% of embryogenic microspores halted their development before the mature embryoid stage. Of these aborted embryogenic microspores, 21% - 33% terminated as multicellular structures, 16% - 19% arrested their development as pre-embryoids, and 7% - 10% halted development as immature embryoids. Identifying factors that are responsible for embryogenic abortion and finding remedy to the issue will help improve the efficiency of doubled haploid production.

The Frequency of Survivorship in Heterozygous Diploids of Cdc13-1exo1Δ Mutants of S. cerevisiae Is One Survivor Cell in 72 Cells/Generation at 36°C

Telomeres cap ends of eukaryotic chromosomes prevent them from degradation and ensure genomic stability. Cdc13 is an essential telomere recruitment and maintenance protein. A temperature-sensitive point mutation in cdc13 gene leads to telomere impairment, giving rise to cdc13-1 mutants that suffer lethality at enhanced temperatures. Deleting Exo1 gene from these mutants, however, leads to the emergence of temperature-tolerant mutants called survivors. Yeasts are known to exist as either diploids or haploids. These yeast genotypes generate survivors. The frequency of survivorship in the haploid genotype is one cell in 104 cells/generation at 36°C, however, the frequency at which they emerge in their diploid counterparts at the same temperature is not known. In this study, we investigated the frequency of Survivorship in heterozygous diploids of cdc13-1exo1Δ mutants of S. cerevisiae at 36°C. Diploids were constructed by mating haploid strains of opposite mating type cdc13-1 exo1:LEU strains with strains of cdc13-1 exo1:HIS. The crosses were 1296 × 3181, 2561 × 3182, 1296 × 3182 and 2561 × 3181. Genetic markers and phenotypic appearance were considered while mating the mutant cells. Using a stick, a smear of one haploid strain was made on each YEPD plate labelled C2, C8, C9, D1, D14, and D15. A smear of another opposite mating type was made on the previous strain. They were mixed and allowed to mate overnight, before culturing on media lacking Luecine and Histidine (-L and -H). Survivors were generated by culturing these diploids at 36°C. Using SPSS 20.0 software for windows SPSS, 2011, the frequency was determined as one Survivor cell in 72 cells/generation, as their frequency of survivorship averaged 5.9 × 10-5 ± 0.04.

Weighted Correlation Network Analysis(WGCNA) of Japanese Flounder(Paralichthys olivaceus) Embryo Transcriptome Provides Crucial Gene Sets for Understanding Haploid Syndrome and Rescue by Diploidization

Artificial gynogenesis is of great research value in fish genetics and breeding technology. However, existing studies did not explain the mechanism of some interesting phenomena. Severe developmental defects in gynogenetic haploids can lead to death during hatching. After diploidization of chromosomes, gynogenetic diploids may dispense from the remarkable malformation and restore the viability, although the development time is longer and the survival rate is lower compared with normal diploids. The aim of this study was to reveal key mechanism in haploid syndrome of Japanese flounder, a commercially important marine teleost in East Asia. We measured genome-scale gene expression of flounder haploid, gynogenetic diploid and normal diploid embryos using RNA-Seq, constructed a module-centric co-expression network based on weighted correlation network analysis(WGCNA) and analyzed the biological functions of correlated modules. Module gene content analysis revealed that the formation of gynogenetic haploids was closely related to the abnormality of plasma proteins, and the up-regulation of p53 signaling pathway might rescue gynogenetic embryos from haploid syndrome via regulating cell cycle arrest, apoptosis and DNA repair. Moreover, normal diploid has more robust nervous system. This work provides novel insights into molecular mechanisms in haploid syndrome and the rescue process by gynogenetic diploidization.

In vitro anther culture and Agrobacterium-mediated transformation of the AP1 gene from Salix integra Linn. in haploid poplar(Populus simonii × P. nigra)

A reliable,efficient anther culture system,the dominant technique for generating haploid plants in breeding programs,that can be used for generating transgenic poplar plants has been needed.In the present study,therefore,an anther culture system was developed using isolated mid-and late-uninucleate anthers of poplar(Populus simonii x P.nigra).From a combination of SSR and ploidy analyses,six double haploid and two haploid lines were characterized from 86 plants grown from 16 regenerated anther cultured lines.After 48 months of development,two plant lines from the regenerated plants maintained their haploid level in vitro for over 2 years.A number of haploid plants from the different lines weretransferred to soil.The leaves of these transplants were then used as explants for transformation with the APETALA1(AP1) gene using Agrobacterium tumefaciens.Overexpression of AP1 in haploid poplar induced early flowering with obvious petals when ectopically expressed.To our knowledge,this is the first report on changes in flowering time in AP1-trangenic poplar,which is important for elucidating the regulatory mechanism of tree flower development.

Analysis of Rice Grain Quality-Associated Quantitative Trait Loci by Using Genetic Mapping

The main objective of this research was to identify quantitative trait loci associated with rice qualities to provide reliable information for marker-assisted selection and development of new varieties. In total, 120 doubled haploid (DH) lines developed by another culture from the F1 hybrid of a cross between “Cheongcheong”, a Tongil variety, and “Nagdong”, a japonica variety, were used. A microsatellite linkage map of 222 markers spanned 2082.4 centimorgans (cM) and covered 12 rice chromosomes with an average interval of 9.4cM between markers. Eight quantitative trait loci (QTLs) were associated with rice quality, consisting of two QTLs on chromosomes 1 and 9 for amylose content;three QTLs on chromosomes 8, 9, and 10 for protein content;and three QTLs on chromosomes 2, 3, and 6 for lipid content. PCR expression levels measured using the SSR markers RM23914 for proteins and RM6266 for lipids, and RM586 showed a higher degree of amplification. The present study should be useful for improving the nutritional quality of rice by means of marker-assisted selection.

Study on Chromosome Doubling for Haploid Produced by Wheat×Maize Crossing

There is no spontaneous chromosome doubling in haploid plants produced by wheat × maize crossing. In order to obtain doubled haploid, two chromosome doubling methods were used. Results showed that: After adding colchicine solution directly into a medium for young embryos that had been cultured 7 days,frequencies of embryo germination in colchicine concentrations of 50lng/L, 100mg/L and 200mg/L were 32.1%, 26.4% and 16.3%, respectively, and frequencies of chromosome doubling were 85.3%, 100% and 50.0%, respectively. But in the control without colchicine, the frequency of embryo germination was 67.4%and no seed was setting. As the time of colchicine treatment increased from 24 to 72 hours, the frequency of embryo germination was reduced, and 24 hours had better results. After soaking seeding crowns and roots with colchicine solution of 500mg/L, 750mg/L and 1 000mg/L for 5 hours, the frequencies of doubling were 89.6%, 76.0% and 73.3%, respectively. By soaking crowns and roots of strong seedings with 500mg/L colchicine solution, the frequency and efficiency of doubling were 98.2% and 93.2%, respectively.

Toward Development of a Whole-genome, BAC/BIBAC-based Integrated Physical/Genetic Map of the Cotton Genome Using the Upland Genetic Standard TM-1: BAG and BIBAC Library Construction, SSR Marker Development, and Physical/Genetic Map Integration

Integrative physical mapping is the centerpieceof and essential for advanced genomics research.Upland cotton(Gossypium hirsutum L.)geneticstandard line TM-1 is used as the referencegenotype to develop a whole-genome,BAC/BIBAC-based integrated physical/genetic map ofthe cotton genome.From the TM-1 line we haveconstructed two BAC libraries with HindIII

Genome size of 14 species of fireflies (Insecta, Coleoptera, Lampyridae)

Eukaryotic genome size data are important both as the basis for comparative research into genome evolution and as estimators of the cost and difficulty of genome sequencing programs for non-model organisms.In this study,the genome size of 14species of fireflies(Lampyridae)(two genera in Lampyrinae,three genera in Luciolinae,and one genus in subfamily incertae sedis)were estimated by propidium iodide(PI)-based flow cytometry.The haploid genome sizes of Lampyridae ranged from0.42 to 1.31 pg,a 3.1-fold span.Genome sizes of the fireflies varied within the tested subfamilies and genera.Lamprigera and Pyrocoelia species had large and small genome sizes,respectively.No correlation was found between genome size and morphological traits such as body length,body width,eye width,and antennal length.Our data provide additional information on genome size estimation of the firefly family Lampyridae.Furthermore,this study will help clarify the cost and difficulty of genome sequencing programs for non-model organisms and will help promote studies on firefly genome evolution.

Nuclear Fusion during Early Stage of Microspore Embryogenesis Indicates Chromosome Doubling in Wheat (Triticum aestivum)

Studies of barley and maize indicate that chromosome doubling occurs via nuclear fusion during an early stage of microspore embryogenesis, but the time and mechanism by which chromosome doubling occurs in bread wheat (Triticum aestivum) remains undetermined. The purpose of this study was to determine the relative time during induction culture when chromosome doubling may occur in wheat, and to identify early indicators for doubled haploid microspores. Microspore nuclei were stained with 4’,6-diamidino-2-phenylindole (DAPI) and observed under a fluorescent microscope on the day of isolation, three days after isolation, and six days after isolation. The change in the percentage of microspores containing a single small nucleus, two small nuclei, a single enlarged nucleus, and three or more nuclei was then tracked throughout the six-day period. Ploidy levels were estimated by determining the cross-sectional area and number of nucleoli in microspores containing small and large nuclei then comparing the results of each respective cell-type. The percentage of microspores containing enlarged nuclei increased throughout the six-day test period, and the percentage of binucleated microspores containing small nuclei decreased. Comparison of the changes in average percentage of microspores containing a single small nucleus, binucleated microspores, microspores containing a single large nucleus, and multinucleate microspores on days 0, 3, and 6 indicates that nuclei classified as “small” are likely haploids and nuclei classified as “large” are doubled haploids. The percentage of microspores with enlarged nucleus (nuclei) during the first six days of induction culture could be used as an early indicator for the frequency of chromosome doubling in wheat microspore culture.