Ming Hao

mRNA and Small RNA Transcriptomes Reveal Insights into Dynamic Homoeolog Regulation of Allopolyploid Heterosis in Nascent Hexaploid Wheat

Newly synthesized allohexaploid wheat lines, which exhibit hybrid vigor or heterosis, may recapitulate the initial genetic state of common wheat. This work shows that, in addition to nonadditive expression, parental expression-level dominance of subgenomes in nascent allohexaploid wheat may contribute distinctively to heterosis through dynamic small RNA–mediated homoeolog regulations. Nascent allohexaploid wheat may represent the initial genetic state of common wheat (Triticum aestivum), which arose as a hybrid between Triticum turgidum (AABB) and Aegilops tauschii (DD) and by chromosome doubling and outcompeted its parents in growth vigor and adaptability. To better understand the molecular basis for this success, we performed mRNA and small RNA transcriptome analyses in nascent allohexaploid wheat and its following generations, their progenitors, and the natural allohexaploid cultivar Chinese Spring, with the assistance of recently published A and D genome sequences. We found that nonadditively expressed protein-coding genes were rare but relevant to growth vigor. Moreover, a high proportion of protein-coding genes exhibited parental expression level dominance, with genes for which the total homoeolog expression level in the progeny was similar to that in T. turgidum potentially participating in development and those with similar expression to that in Ae. tauschii involved in adaptation. In addition, a high proportion of microRNAs showed nonadditive expression upon polyploidization, potentially leading to differential expression of important target genes. Furthermore, increased small interfering RNA density was observed for transposable element–associated D homoeologs in the allohexaploid progeny, which may account for biased repression of D homoeologs. Together, our data provide insights into small RNA–mediated dynamic homoeolog regulation mechanisms that may contribute to heterosis in nascent hexaploid wheat.

Production of hexaploid triticale by a synthetic hexaploid wheat-rye hybrid method

Hexaploid triticale, including its primary and secondary forms, is an important forage crop and a promising energy plant. Primary forms are usually developed by crossing Triticum turgidum L. with rye, with secondary forms obtained by crossing primary hexaploid triticale and/or hexaploid wheat with octoploid triticale. In this study, we developed an effective method for production of hexaploid triticale via hybridization of synthetic hexaploid wheat (SHW) with rye. The three employed SHW lines were derived from hybridization of T. turgidum with Aegilops tauschii Cosson, and inherited meiotic restitution genes, which can promote the formation of functional gametes in haploid status, from their T. turgidum parents. Although the resulting tetraploid F1 hybrids with rye (genome ABDR) produced amphiploids (octoploid triticale) and partial amphiploids, the final hybrid products obtained through fertility selection over several generations were hexaploids. These hexaploids were the result of preferential elimination of D-genome chromosomes. In addition to complete hexaploid triticale with 28 intact A/B and 14 intact R chromosomes, we obtained hexaploid triticales with other chromosome constitutions, including monosomic, substitution, and translocation lines. Chromosomes 2D and 5D from the wild species A. tauschii were incorporated into the hexaploid triticales. Out of eight analyzed stable lines derived from three different SHW-L1/rye F1 plants, we observed four lines with small-fragment translocations between wheat and rye chromosomes. Rapid production of hexaploid triticales using this method involves two factors: (1) hybridization between hexaploid wheat with a meiotic restitution gene(s) and rye and (2) selection for good fertility during F3 and subsequent generations.

Microsatellite Mutation Rate during Allohexaploidization of Newly Resynthesized Wheat

Simple sequence repeats (SSRs, also known as microsatellites) are known to be mutational hotspots in genomes. DNA rearrangements have also been reported to accompany allopolyploidization. A study of the effect of allopolyploidization on SSR mutation is therefore important for understanding the origin and evolutionary dynamics of SSRs in allopolyploids. Three synthesized double haploid (SynDH) populations were made from 241 interspecific F1 haploid hybrids between Triticum turgidum L. and Aegilops tauschii (Coss.) through spontaneous chromosome doubling via unreduced gametes. Mutation events were studied at 160 SSR loci in the S1 generation (the first generation after chromosome doubling) of the three SynDH populations. Of the 148260 SSR alleles investigated in S1 generation, only one mutation (changed number of repeats) was confirmed with a mutation rate of 6.74 × 10−6. This mutation most likely occurred in the respective F1 hybrid. In comparison with previously reported data, our results suggested that allohexaploidization of wheat did not increase SSR mutation rate.

Genetic map of Triticum turgidum based on a hexaploid wheat population without genetic recombination for D genome

BackgroundA synthetic doubled-haploid hexaploid wheat population, SynDH1, derived from the spontaneous chromosome doubling of triploid F1 hybrid plants obtained from the cross of hybrids Triticum turgidum ssp. durum line Langdon (LDN) and ssp. turgidum line AS313, with Aegilops tauschii ssp. tauschii accession AS60, was previously constructed. SynDH1 is a tetraploidization-hexaploid doubled haploid (DH) population because it contains recombinant A and B chromosomes from two different T. turgidum genotypes, while all the D chromosomes from Ae. tauschii are homogenous across the whole population. This paper reports the construction of a genetic map using this population.ResultsOf the 606 markers used to assemble the genetic map, 588 (97%) were assigned to linkage groups. These included 513 Diversity Arrays Technology (DArT) markers, 72 simple sequence repeat (SSR), one insertion site-based polymorphism (ISBP), and two high-molecular-weight glutenin subunit (HMW-GS) markers. These markers were assigned to the 14 chromosomes, covering 2048.79 cM, with a mean distance of 3.48 cM between adjacent markers. This map showed good coverage of the A and B genome chromosomes, apart from 3A, 5A, 6A, and 4B. Compared with previously reported maps, most shared markers showed highly consistent orders. This map was successfully used to identify five quantitative trait loci (QTL), including two for spikelet number on chromosomes 7A and 5B, two for spike length on 7A and 3B, and one for 1000-grain weight on 4B. However, differences in crossability QTL between the two T. turgidum parents may explain the segregation distortion regions on chromosomes 1A, 3B, and 6B.ConclusionsA genetic map of T. turgidum including 588 markers was constructed using a synthetic doubled haploid (SynDH) hexaploid wheat population. Five QTLs for three agronomic traits were identified from this population. However, more markers are needed to increase the density and resolution of this map in the future study.

Comparison of homoeologous chromosome pairing between hybrids of wheat genotypes Chinese Spring ph1b and Kaixian-luohanmai with rye

The ph-like genes in the Chinese common wheat landrace Kaixian-luohanmai (KL) induce homoeologous pairing in hybrids with alien species. In the present study, meiotic phenotypic differences on homoeologous chromosome pairing at metaphase I between hybrids of wheat genotypes Chinese Spring ph1b (CSph1b) and KL with rye were studied by genomic in situ hybridization (GISH). The frequency of wheat-wheat associations was higher in CSph1b×rye than in KL×rye. However, frequencies of wheat-rye and rye-rye associations were higher in KL×rye than in CSph1b×rye. These differences may be the result of different mechanisms of control between the ph-like gene(s) controlling homoeologous chromosome pairing in KL and CSph1b. Wheat-wheat associations were much more frequent than wheat-rye pairing in both hybriods. This may be caused by lower overall affinity, or homoeology, between wheat and rye chromosomes than between wheat chromosomes.

Distant Hybridization: A Tool for Interspecific Manipulation of Chromosomes

Wide or distant hybridization has been widely used as an important tool of chromosome manipulation for crop improvement. The chromosome behaviors in F1 hybrids provide us with the essential genetic basis for chromosome manipulation. The induction of homoeologous pairing in F1 hybrid plants followed by the incorporation of a single-chromosome fragment from an alien or a wild species into an existing crop species by translocating chromosomes has been used in the production of translocation lines. Most efforts to transfer a beneficial trait from wild plants into crops so far have bridged the species gap via alien chromosome translocation lines. Chromosome doubling in somatic cells or gametes of F1 hybrids followed by the incorporation of all alien chromosomes has been used in the production of amphidiploids. Amphidiploidy can be used for a bridge to move a single chromosome from one species to another or for the development of new crops. Chromosome elimination of a uniparental genome during the development of F1 hybrid embryos has been used in the production of haploids. Haploids are very useful in double-haploid breeding of a true-breeding crop such as wheat and rice since this method can quickly replace genetic recombination while enhancing breeding efficiency or facilitating genetic analysis.

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 F(1)s. 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 (Triticum aestivum L.) and molecular markers were used to demonstrate the SynDH method.

QTug.sau-3B is a major quantitative trait locus for wheat hexaploidization

Meiotic nonreduction resulting in unreduced gametes is thought to be the predominant mechanism underlying allopolyploid formation in plants. Until now, however, its genetic base was largely unknown. The allohexaploid crop common wheat (Triticum aestivum L.), which originated from hybrids of T. turgidum L. with Aegilops tauschii Cosson, provides a model to address this issue. Our observations of meiosis in pollen mother cells from T. turgidum×Ae. tauschii hybrids indicated that first division restitution, which exhibited prolonged cell division during meiosis I, was responsible for unreduced gamete formation. A major quantitative trait locus (QTL) for this trait, named QTug.sau-3B, was detected on chromosome 3B in two T. turgidum×Ae. tauschii haploid populations. This QTL is situated between markers Xgwm285 and Xcfp1012 and covered a genetic distance of 1 cM in one population. QTug.sau-3B is a haploid-dependent QTL because it was not detected in doubled haploid populations. Comparative genome analysis indicated that this QTL was close to Ttam-3B, a collinear homolog of tam in wheat. Although the relationship between QTug.sau-3B and Ttam requires further study, high frequencies of unreduced gametes may be related to reduced expression of Ttam in wheat.

Cytological identification of an Aegilops variabilis chromosome carrying stripe rust resistance in wheat

Aegilops variabilis (UUSvSv), an important sources for wheat improvement, originated from chromosome doubling of a natural hybrid between Ae. umbellulata (UU) with Ae. longissima (SlSl). The Ae. variabilis karyotype was poorly characterized by fluorescent in situ hybridization (FISH). The FISH probe combination of pSc119.2, pTa71 and pTa-713 identified each of the 14 pairs of Ae. variabilis chromosomes. Our FISH ideogram was further used to detect an Ae. variabilis chromosome carrying stripe rust resistance in the background of wheat lines developed from crosses of the stripe rust susceptible bread wheat cultivar Yiyuan 2 with a resistant Ae. variabilis accession. Among the 15 resistant BC1F7 lines, three were 2Sv + 4Sv addition lines (2n = 46) and 12 were 2Sv(2B) or 2Sv(2D) substitution lines that were confirmed with SSR markers. SSR marker gwm148 can be used to trace 2Sv in common wheat background. Chromosome 2Sv probably carries gametocidal(Gc) gene(s) since cytological instability and chromosome structural variations, including non-homologous translocations, were observed in some lines with this chromosome. Due to the effects of photoperiod genes, substitution lines 2Sv(2D) and 2Sv(2B) exhibited late heading with 2Sv(2D) lines being later than 2Sv(2B) lines. 2Sv(2D) substitution lines were also taller and exhibited higher spikelet numbers and longer spikes.

The genetic study utility of a hexaploid wheat DH population with non-recombinant A- and B-genomes

To study the D-genome of the wild wheat relative Aegilops tauschii Cosson at the hexaploid level, we developed a synthetic doubled-haploid (DH) hexaploid wheat population, SynDH3. This population was derived from the spontaneous chromosome doubling of triploid F1 hybrid plants obtained from a cross between Triticum turgidum ssp. dicoccon PI377655 and A. tauschii ssp. strangulata AS66 × ssp. tauschii AS87. SynDH3 is a diploidization-hexaploid DH population containing recombinant D chromosomes from two different A. tauschii genotypes, with A and B chromosomes from T. turgidum being homogenous across the entire population. Using this population, we constructed a genetic map. Of the 440 markers used to construct the map, 421 (96%) were assigned to 12 linkage groups; these included 346 Diversity Arrays Technology (DArT) and 75 simple sequence repeat (SSR) markers. The total map length of the seven D chromosomes spanned 916.27 cM, with an average length of 130.90 cM per chromosome and an average distance between markers of 3.47 cM. Seven segregation distortion regions were detected on seven linkage groups. Out of 50 markers shared with those on a common wheat map, 37 showed a consistent order. The utility of the diploidization-hexaploid DH population for mapping qualitative trait genes was confirmed using the dominant glaucousness-inhibiting gene W2I as an example.