Structural chromosome variations (SCVs) are large-scale genomic variations that can be detected by fluorescence in situ hybridization (FISH). SCVs have played important roles in the genome evolution of wheat (Triticum aestivum L.), but little is known about their genetic effects. In this study, a total of 543 wheat accessions from the Chinese wheat mini-core collection (CWMCC) and Shanxi Province wheat collection (SXPWC) were used for chromosome analysis using oligonucleotide probe multiple (ONPM) FISH. A total of 139 SCVs including translocations, pericentric inversions, presence/absence variations (PAVs), and copy number variations (CNVs) in heterochromatin were identified at 230 loci. The distribution frequency of SCVs varied between ecological regions and between landraces and modern cultivars. Structural analysis using SCVs as markers clearly divided the landraces and modern cultivars into different groups. There are very clear instances illustrating alien introgression and wide application of foreign germplasms improved the chromosome diversity of Chinese modern wheat cultivars. Genome wide association study (GWAS) identified 29 SCVs associated with 12 phenotypic traits, and five (RT4AS•4AL-1DS/1DL•1DS-4AL, Mg2A-3, Mr3B-10, Mr7B-13, and Mr4A-7) of them were further validated using a DH population and advanced sib-lines, implying the potential value of these SCVs. Importantly, the number of favored SCVs that associated with agronomic trait improvement was significantly higher in modern cultivars compared to landraces, indicating positive selection in wheat breeding. This study demonstrates the significant effects of SCVs during wheat breeding and provides an efficient method of mining favored SCVs in wheat and other crops.

Genome wide association study reveals structural chromosome variations (SCVs) with phenotypic effects in wheat (Triticum aestivum L.).

Knowledge of short-term physiological adaption of wheat to soil water deficit is well understood, but little is known about seed ethephon priming effect on stress memory against drought at the tillering stage of wheat. The 42 leading and modern cultivars released between 1991 and 2012 were subjected to drought (45% Field water-holding capacity), and well-watered (75% Field water-holding capacity) for 3 weeks to evaluate the genetic progress of wheat against drought stress. Seeds of the drought-sensitive cultivar (CM104) primed with ethephon were subjected to soil water deficit and well-watered to uncover ethephon-induced stress responses at organic, cellular, and molecular levels. Soil water deficit (45% FC) occurred at the tillering stage resulted in 3.2 to 67.4% yield loss, and genetic improvement of wheat against drought resulted in the yield loss decreased at a rate of 0.70% per year, which was determined mainly by fertile spike. Seed ethephon priming maintained leaf water under soil water deficit at the tillering stage by improving root volume and dry weight, which maintained leaf water and improved the drought avoidance capability of wheat. Seed ethephon priming decreased leaf malondialdehyde content by regulating root ERF, root to leaf ABA signaling, leaf ROS-scavenging capability, and leaf osmotic regulation, which improved the drought tolerance capability of dryland wheat. Comparative root tips transcriptome analysis revealed that differentially expressed genes and pathways involved in ethylene-induced drought tolerance are associated with carbon metabolism, glutathione metabolism, and phenylpropanoid biosynthesis. At maturity, seed ethephon priming increased fertile spikes and reduced spikelets abortion, which provided extra 0.3 t ha−1 of grain yield. These results suggested that seed ethephon priming allowed the recall of long-lasting stress defensive memory, increasing fertile spikes and grain yield by both drought avoidance and drought tolerance.

Genetic improvement combined with seed ethephon priming improved grain yield and drought resistance of wheat exposed to soil water deficit at tillering stage

https://link.springer.com/content/pdf/10.1007/s12229-021-09274-y.pdf

Estimation of genetic diversity and its exploitation in plant breeding

OUP accepted manuscript

Wheat landrace Yanda 1817 is one of the 'core parental' breeding lines for North China Winter Wheat Breeding Program during 1950-1960. The derivatives of cross Triumph/Yanda 1817 have been widely planted in the area and, thereafter, used as parental lines to make further crosses for new varieties development. In this study, the genetic contributions of core parental lines Yanda 1817 and Triumph to their derivative cultivars were analyzed using 175 polymorphic SSR markers randomly distributed on the 21 chromosomes of wheat genome with an average of 8.3 markers per chromosome. The results indicated that Triumph (43.6%) contributed more genetic components than Yanda 1817 (26.8%) to their derivatives on the whole genome level. On the A, and D subgenome levels, triumph had the contribution ratio of 46.1%, 39.1%, and 44.0%, while Yanda 1817 only had the contribution ratio of 25.9%, 25.7%, and 26.4% to their derivatives, respectively. It revealed that exogenous germplasm played an important role in the improvement of wheat varieties in the North China Winter Wheat Breeding Program. As for single chromosomes, 20.0% (1A) to 63.3% (7A) of Triumph alleles and 7.5% (2A) to 44.2% (7D) of Yanda 1817 alleles could be detected on the derivative cultivars. Seven Yanda 1817 genomic (haplotypic) regions, Xwmc11-3A-Xcfa2262, Xbarc1073-7B-Xwmc475, Xgwm357-1AL-Xwmc312, Xbarc305-7DS-Xwmc506, Xgwm165-4AS-Xgwm610, Xwmc419-1 B-Xwmc134, and Xcfd56-2D-Xbarc228, and eight Triumph genomic (haplotypic) regions, Xwmc105-6BS-Xwmc397, Xgdm72-3D-Xgdm8, Xgdm5-2DS-Xgwm455, Xbarc121-7AL-Xgwm332, Xgwm174-5DL-Xwmc161, Xgwm499-5BL-Xbarc308, Xbarc141-5A-Xgwm291, and Xgwm66-4BL-Xgwm251, were found to be significantly important in the Triumph/Yanda 1817 derivative cultivars. Genomic (haplotypic) regions Xwmc11-3A-Xcfa2262 derived from Yanda 1817 and Xwmc105-6BS-Xwmc397 derived from Triumph had the contribution ratio of 77.5% and 71.3%, respectively to the derivative cultivars of Triumph/Yanda 1817, indicating they are important targets for selection in breeding program. Agronomic important genes and QTLs relevant to yield, disease resistance, tolerance to abiotic stresses and adaptation to diversified environments located on these genomic (haplotypic) regions are important targets for new varieties development in the North China Winter Wheat Breeding Program.

小麦骨干亲本“胜利麦／燕大1817”杂交组合后代衍生品种遗传构成解析

Founder wheat lines have played key role in Chinese wheat improvement. Wheat-Dasypyrum villosum translocation T6VS·6AL has been widely used in wheat breeding in recent years due to its high level of powdery mildew resistance and other beneficial genes. Reference oligo-nucleotide multiplex probe (ONMP)–FISH karyotypes of six T6VS·6AL donor lines were developed and used for characterizing 32 derivative cultivars and lines. T6VS·6AL was present in 27 cultivar/lines with 20 from southern China. Next, ONMP–FISH was used to study chromosome constitution of randomly collected wheat cultivars and advanced breeding lines from southern and northern regions of China: 123 lines from the regional test plots of southern China and 110 from northern China. In southern China, T6VS·6AL (35.8%) was the most predominant variation, while T1RS·1BL (27.3%) was the most predominant in northern China. The pericentric inversion perInv 6B derived from its founder wheat Funo and Abbondaza was the second most predominant chromosome variant in both regions. Other chromosome variants were present in very low frequencies. Additionally, 167 polymorphic chromosome types were identified. Based on these variations, 271 cultivars and lines were clustered into three groups, including southern, northern, and mixed groups that contained wheat from both regions. Different dominant chromosome variations were seen, indicating chromosome differentiation in the three groups of wheat. The clearly identified wheat lines with T6VS·6AL in different backgrounds and oligonucleotide probe set will facilitate their utilization in wheat breeding and in identifying other beneficial traits that may be linked to this translocation.

Predominant wheat-alien chromosome translocations in newly developed wheat of China

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Predominant wheat-alien chromosome translocations in newly developed wheat of China