Lianquan Zhang

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.

Synthetic hexaploid wheat and its utilization for wheat genetic improvement in China

Synthetic hexaploid wheat (Triticum turgidumxAegilops tauschii) was created to explore for novel genes from T. turgidum and Ae. tauschii that can be used for common wheat improvement. In the present paper, research advances on the utilization of synthetic hexaploid wheat for wheat genetic improvement in China are reviewed. Over 200 synthetic hexaploid wheat (SHW) accessions from the International Maize and Wheat Improvement Centre (CIMMYT) were introduced into China since 1995. Four cultivars derived from these, Chuanmai 38, Chuanmai 42, Chuanmai 43 and Chuanmai 47, have been released in China. Of these, Chuanmai 42, with large kernels and resistance to stripe rust, had the highest average yield (>6 t/ha) among all cultivars over two years in Sichuan provincial yield trials, outyielding the commercial check cultivar Chuanmai 107 by 22.7%. Meanwhile, by either artificial chromosome doubling via colchicine treatment or spontaneous chromosome doubling via a union of unreduced gametes (2n) from T. turgidum-Ae. tauschii hybrids, new SHW lines were produced in China. Mitotic-like meiosis might be the cytological mechanism of spontaneous chromosome doubling. SHW lines with genes for spontaneous chromosome doubling may be useful for producing new SHW-alien amphidiploids and double haploid in wheat genetic improvement.

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 occurred 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 chromosome 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 ployploidization. The rapid and directional changes at the early stage of polyploidization might contribute to the rapid evolution of the newly formed allopolyploid and allow the divergent genomes to act in harmony.

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.

Production of aneuhaploid and euhaploid sporocytes by meiotic restitution in fertile hybrids between durum wheat Langdon chromosome substitution lines and Aegilops tauschii

Fertile F(1) hybrids were obtained between durum wheat (Triticum durum Desf.) Langdon (LDN) and its 10 disomic substitution (LDN DS) lines with Aegilops tauschii accession AS60 without embryo rescue. Selfed seedset rates for hybrids of LDN with AS60 were 36.87% and 49.45% in 2005 and 2006, respectively. Similar or higher selfed seedset rates were observed in the hybrids of 1D (1A), 1D (1B), 3D (3A), 4D (4B), 7D (7A), and 2D (2B) with AS60, while lower in hybrids of 3D (3B) + 3BL, 5D (5A) + 5AL, 5D (5B) + 5B and 6D (6B) + 6BS with AS60 compared with the hybrids of LDN with AS60. Observation of male gametogenesis showed that meiotic restitution, both first-division restitution (FDR) and single-division meiosis (SDM) resulted in the formation of functional unreduced gametes, which in turn produced seeds. Both euhaploid and aneuhaploid gametes were produced in F(1) hybrids. This suggested a strategy to simultaneously transfer and locate major genes from the ancestral species T. turgidum or Ae. tauschii. Moreover, there was no significant difference in the aneuhaploid rates between the F(1) hybrids of LDN and LDN DS lines with AS60, suggesting that meiotic pairing between the two D chromosomes in the hybrids of LDN DS lines with AS60 did not promote the formation of aneuhaploid gametes.

Different maternal genome donor to Kengyilia species inferred from chloroplast trnL-F sequences

To reveal the maternal donor of species in genus Kengyilia, the chloroplast trnL-F sequences of 14 Kengyilia species and several related diploid species were analyzed by using Maximum Parsimony (MP) and Bayesian Inference (BI) methods. The species in Kengyilia were clustered in different clades, which indicated that Agropyron (P) is the likely maternal genome donor to Kengyilia melanthera, K. mutica and K. thoroldiana, while the maternal donor to Kengyilia batalinii, K. nana, K. kokonorica, K. kaschgarica, K. hirsuta, K. alatavica, K. gobicola, K. zhaosuensis, K. rigidula, K. longiglumis and K. grandiglumis was St or Y Roegneria genome.

Relationships among Leymus species assessed by RAPD markers

The DNA genetic diversity of 40 accessions of genus Leymus was analyzed by random amplified polymorphic DNA (RAPD) markers. A total of 352 products were amplified by 34 10-mer arbitrary primers, among which 337 products (95.74 %) were found to be polymorphic. 5–14 polymorphic bands were amplified by each polymorphic primer, with an average of 9.91 bands. The data of 352 RAPD bands were used to generate Jaccard’s similarity coefficients and to construct a dendrogram by means of UPGMA. Great genetic diversity in genus Leymus was observed, the genetic diversity among the different species more abundant than that of the different accessions, and the different accessions in a species or the species from the same areas were clustered together.

Allelic variation and distribution of HMW glutenin subunit 1Ay in Triticum species

The allelic variation and distribution of high-molecular-weight (HMW) glutenin subunit 1Ay in 814 Triticum lines were investigated by sodium dodecyl sulfate polyacrylamide-gel electrophoresis (SDS–PAGE). 1Ay subunit existed in 13 out of analyzed 21 species. The four species T. turgidum L., T. polonicum L., T. turanicum Jakubz. and T. zhukovskyi Men. et Er. were firstly discovered with expressed 1Ay subunit. The distribution frequencies for diploid, tetraploid and hexaploid wheats were at 87.89, 20.31 and 1.79%, respectively. Among the observed eight 1Ay alleles, three with the electrophoretic mobilities similar to 1Bx6, 1By8, and between 1By8 and 1Dy10 were firstly observed. Five had the mobilities similar to 1Bx6, 1Bx7, 1By8, 1Dy10, and 1Dy12 in Glu-1B and Glu-1D loci of hexaploid wheat. It is very difficult to distinguish these 1Ay alleles in Glu-1Ay from those in hexaploid wheat. The predominant 1Ay alleles were those with the mobilities similar to 1Bx7, 1By8, 1Dy10 and 1Dy12, and faster than 1Dy12. Comparison results of 1Ay alleles in different species indicated that multiple diploid lines were involved in the evolution process of tetraploid wheat. The 1Ay allelic variations and genetic resources might be useful in the quality improvement of common wheat.

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.