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This article introduces Kihara’s main achievements in wheat cytogenetics and the succeeding developments in a few fields of wheat cytogenetics, which were founded by Kihara. Following the discovery of polyploidy in wheat by Sakamura (Bot Mag (Tokyo) 32:150–153, 1918), Kihara established the cytogenetics of interploid hybrids, clarifying the meiotic chromosome behavior as well as the chromosome number and genome constitution of their progeny, based on which Kihara formulated the concept of genome. Here, evidence supporting his recognition of the genome as a functional unit is presented. Kihara proposed the methodology for genome analysis and determined the genome constitution of all and species. Ohta re-evaluated the genome relationships among the diploid species, using the B-chromosomes of . After completing the genome analyses, Kihara’s interest was shifted to the genome-plasmon interaction that led to the discovery of cytoplasmic male sterility in wheat. Using the nucleus substitution method elaborated by Kihara, we carried out plasmon analysis of and species. We classified their plasmons into 17 major types and 5 subtypes and determined the maternal and paternal lineages of all polyploid species. An alloplasmic line, ()-Tve, retained male sterility induction and germless grain production for 60 generations of backcrosses with wheat pollen. We are trying reconstruction of the plant from the genome of its native strain and the plasmon in the alloplasmic wheat. Two groups of Kihara’s school reported paternal transmission of the mtDNA sequences in alloplasmic wheats. Their findings are incompatible with the genetic autonomy of the plasmon, casting a new challenge to the genome-plasmon interaction.

In 1935, the work of Japanese scientist Gonjiro Inazuka to cross a semi-dwarf Japanese wheat landrace with two American varieties resulted in an improved semi-dwarf variety, known as Norin 10. Unlike other varieties, which stood taller than 150 cm, the and genes present in Norin 10 reduced its height to 60–110 cm. In the late 1940s Orville Vogel at Washington State University used Norin 10 to help produce high-yielding, semi-dwarf winter wheat varieties. Eventually, Vogel’s varieties ended up in the hands of Norman Borlaug, who was working to develop rust-resistant wheat in Mexico.

The political framework and the development of molecular biology and electronic data management caused a general paradigm shift in plant genetic resources (PGR), exemplified here for wheat. (1) versus maintenance of PGR. maintenance lost predominance. Wild wheats are effectively maintained in the wild; landraces do well on farm. New methods did not lead to the expected progress. (2) Inclusion of neglected and underutilized crop species. Some species are probably extinct in traditional cultivation areas, whereas landraces were recently found for others. Wild relatives have gained importance in wheat breeding: besides wild species, also , , and other genera are used. × reached world importance; × will follow soon. (3) Methods of analysing diversity within and between taxa. New technology yields new insights in the structure and evolution of populations. (4) Genetic erosion is a problem, also inside genebanks. (5) Landraces show complex morphological diversity. Infraspecific classification systems are useful for their characterization and handling, but less recognised by breeders. (6) Methods of evaluation. Molecular markers identify genetic differences on a fairly simple level without reference to ecological adaptation. (7) Genebanks should expand classical evaluation programmes. Pre-breeding will gain importance. (8) Storage and reproduction in genebanks is done effectively and cost-efficiently under long-term conditions, but strategic concepts for reproduction are needed. Traditional methods are often neglected, and modern possibilities over-emphasized. Maintenance of landraces in genebanks and on farm poses challenges. PGR work is conservative. Landraces can be studied by traditional methods; molecular methods can resolve specific questions.

Plant genetic resources, the source of genetic diversity provides a broad genetic foundation for plant breeding and genetic research, however, large germplasm resources are difficult to preserve, evaluate and use. Construction of core and mini core collections is an efficient method for managing genetic resources and undertaking intensive surveys of natural variation, including the phenotyping of complex traits and genotyping of DNA polymorphisms allowing more efficient utilization of genetic resources. A mega characterization and evaluation programme of the entire cultivated gene pool of wheat conserved in the National Genebank, India was undertaken. Wheat accessions with limited seed quantity, were multiplied in the off-season nursery at IARI Regional Station, Wellington during rainy season 2011 and the entire set of 22,469 wheat accessions were characterized and evaluated at CCS HAU, Hisar, Haryana during winter season 2011–12 for 34 characters including 22 highly heritable qualitative, and 12 quantitative parameters. The core sets were developed using PowerCore Software with stepwise approach and grouping method and validated using Shannon-Diversity Index and summary statistics. Based on Shannon-Diversity index, PowerCore with stepwise approach was found better than PowerCore with grouping. The core set included 2,208 accessions comprising 1,770 , 386 , and 52 accessions as a representative of the total diversity recorded in the wheat germplasm. The core set developed will be further validated at different agro-climatic conditions and will be utilized for development of mini core set to enhance the utilization by wheat researchers and development of climate resilient improved varieties.

Stem rust resistance genes have been found in four different sources of . These include diploid accessions AEG357-4 and AEG874-60 and the amphiploids Chinese Spring/ TA8026 and TS01. Stem rust resistance was mapped to the 2S chromosomes derived from each of these lines. The previously reported 2B-2S#3 translocation derived from AEG357-4 was found to carry two stem rust resistance genes, here temporarily named and . The resistance genes found on the 2S chromosomes each derived from TA8026, TS01 and AEG874-60 are named , and , respectively. Lines carrying genes and are being distributed to wheat breeding programs around the world.

L. is a diploid wild relative of wheat with the main distribution in the northeastern Mediterranean basin from Greece to northern Iraq. Two varieties are taxonomically described in this species based on spike morphology. In the present work, to elucidate the geographical differentiation pattern of the species, the geographical distribution of the two varieties was reviewed, 35 accessions derived from the entire distribution area were crossed with the four Tester lines, two varieties derived from their sympatric stands on the Aegean Islands were crossed with each other, and their F, F and/or BCF populations were examined. It became clear that the present distribution area of can be divided into the western and eastern regions with the border in the mountains lying between West Anatolia and Central Anatolia: the western and eastern accessions are isolated not only geographically but also reproductively by hybrid sterility caused by gametocidal-like genes, and the morphology of var. is controlled by two different genotypes in the western and eastern regions. It was suggested that occurred in the two isolated refuges during the maximum glacial period, the Aegean region and the western Levant or some sheltered habitats in the East Taurus/Zagros mountains arc, and that the latter population now occurs in the eastern region while the former now occupies the western region of the distribution.

The 13th International Wheat Genetics Symposium (IWGS) is being held in the year I begin my phased retirement, marking a career of 40 years in wheat genetics, beginning with a postdoctoral fellowship in 1973 with Ernie Sears and Gordon Kimber at Columbia, Missouri, then the premier center for wheat chromosome research. I was fortunate to have won a DF Jones fellowship for my research proposal, “Exploration and application of the Quinacrine and Giemsa staining technique in the genus ” that led to the cytogenetic identification of wheat and rye chromosomes (Gill and Kimber 1974a, b). In 1973, I also attended, for the first time, the meetings of the 4th IWGS in Columbia, Missouri, and was in awe of the research presentations and heated discussions on wheat evolution. In 1979, I established my own research group and laboratory at Kansas State University focusing on wheat chromosome mapping and manipulation for crop improvement under the auspices of Wheat Genetics Resource Center (reviewed in Raupp and Friebe, Plant Breed Rev 37:1–34, 2013). Among the first visitors to my laboratory were Takashi Endo, then at Nara University, Japan, and Chen Peidu, from Nanjing Agricultural University, and presented this research at the 6th IWGS in Kyoto, Japan. Therefore, it is a special feeling to be returning to Japan for a farewell presentation. My intent is to briefly review the history of wheat chromosome research and how our laboratory played a role in advancing wheat chromosome analysis leading to the chromosome survey sequencing paper utilizing telosomic stocks (IWGSC, Science 345:285–287, 2014).

Chromosomal structural changes can be induced by the addition of specific alien chromosomes called ‘gametocidal (Gc) chromosomes’. In the monosomic addition of the Gc chromosome to common wheat, chromosomal breaks occur in gametes receiving no Gc chromosome, and the broken ends heal and stabilize in the subsequent generations. Thus, by the so-called Gc system, deficiencies and translocations can be induced in common wheat and also in alien chromosome addition and substitution lines of common wheat. Deficiencies of wheat and alien chromosomes were cytologically identified by the chromosome banding and in situ hybridization techniques. The plants carrying deletions or wheat-alien translocations were established as new aneuploid lines of common wheat with sub-arm aneuploidy. Those for wheat chromosomes are called deletion stocks and those for alien chromosomes are called dissection lines. The new aneuploids have been used for cytological chromosome mapping and have corrected some mistakes in genetic mapping.

Polyploid wheats are represented by two evolutionary lineages – Emmer and Timopheevi. It was reported that the species of these groups differentiated by species-specific translocations; they showed distinct karyotype structures, i.e., the amount and the distribution of heterochromatin. Analysis of more than 1,500 accessions representing 21 wild and cultivated polyploid wheat species using C-banding revealed that intra- and interspecific divergence within these two groups was accompanied by chromosomal rearrangements. Intraspecific diversity was the highest for wild species, followed by landraces and commercial cultivars. Chromosomal rearrangements were more frequent in than in (55.7 % and 35.3 % correspondingly) Altogether, 2 pericentric inversions, 28 single translocations, 13 double translocations, and five multiple translocations were identified in 150 of 270 accessions. Sixty types of chromosomal rearrangements (4 inversions, 37 single translocations, 11 double and 6 triple translocations, and two unclassified rearrangements) were found in (143 of 400 accessions). The range of karyotype diversity decreased in cultivated Emmer: 25 single translocations, 4 pericentric inversions, 6 double and 3 multiple translocations were detected in 119 of 470 accessions (24.5 %). The translocation T5B:7A significantly dominated over other variants; alone or in combination with other translocations, being identified in 51 lines of (Schrank) Schübler, preferentially from Western Europe and Mediterranean countries. Chromosomal rearrangements were also found in common wheat, the translocations T5B:7B and wheat-rye T1RS:1BL being the most frequent (25 and 29 cultivars respectively). In addition to them, 24 variants of chromosomal rearrangements, including inversions, single and multiple translocations and wheat-alien translocations and substitutions were discovered in 112 of 295 cultivars we studied.

Although shotgun sequences of the genomic DNA of common wheat and its ancestors are available, gene discovery in common wheat is primarily based on proof sequencing of expressed full-length (FL) cDNAs. Use of expressed sequence tag (EST) databases including FLcDNA has been recognized as an important method for gene annotation in common wheat. In the large repetitive genome of common wheat, a transcriptome approach is complementary to whole genome sequencing. We have initiated a wheat EST project in Japan and constructed cDNA libraries from various tissues and strains of wheat, including biotic and abiotic stress treatments. We have also generated a high quality full-length cDNA resource for common wheat, an essential element necessary for the ongoing curation and annotation of the wheat genome. After several rounds of screening of CAP-trapped cDNA libraries, 21,408 FLcDNAs have been fully sequenced. The origins of these FLcDNAs were estimated through examination of the RNAseq data of three ancestral diploids, namely, , , and . In addition, 51 cDNA libraries were constructed with an accumulation of 0.9 million ESTs. The ESTs, including the FLcDNA data, were assembled into contigs with stringent bioinformatic tool parameters. In total, 41,003 gene clusters were classified, in which 27,943 (68.1 %) had homology with other cereal genes. The digital monitoring system was utilized to identify characteristic gene expression patterns among various tissues and stress treatments in common wheat. These transcriptome data comprise a substantial reference for wheat genome sequencing.