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The rapid development and application of molecular marker assays have facilitated genomic selection and genome‐wide linkage and association studies in wheat breeding. Although PCR‐based markers (e.g. simple sequence repeats and functional markers) and genotyping by sequencing have contributed greatly to gene discovery and marker‐assisted selection, the release of a more accurate and complete bread wheat reference genome has resulted in the design of single‐nucleotide polymorphism (SNP) arrays based on different densities or application targets. Here, we evaluated seven types of wheat SNP arrays in terms of their SNP number, distribution, density, associated genes, heterozygosity and application. The results suggested that the Wheat 660K SNP array contained the highest percentage (99.05%) of genome‐specific SNPs with reliable physical positions. SNP density analysis indicated that the SNPs were almost evenly distributed across the whole genome. In addition, 229 266 SNPs in the Wheat 660K SNP array were located in 66 834 annotated gene or promoter intervals. The annotated genes revealed by the Wheat 660K SNP array almost covered all genes revealed by the Wheat 35K (97.44%), 55K (99.73%), 90K (86.9%) and 820K (85.3%) SNP arrays. Therefore, the Wheat 660K SNP array could act as a substitute for other 6 arrays and shows promise for a wide range of possible applications. In summary, the Wheat 660K SNP array is reliable and cost‐effective and may be the best choice for targeted genotyping and marker‐assisted selection in wheat genetic improvement.

Summary The incorporation of resistance genes into wheat commercial varieties is the ideal strategy to combat stripe or yellow rust (YR). In a search for novel resistance genes, we performed a large‐scale genomic association analysis with high‐density 660K single nucleotide polymorphism (SNP) arrays to determine the genetic components of YR resistance in 411 spring wheat lines. Following quality control, 371 972 SNPs were screened, covering over 50% of the high‐confidence annotated gene space. Nineteen stable genomic regions harbouring 292 significant SNPs were associated with adult‐plant YR resistance across nine environments. Of these, 14 SNPs were localized in the proximity of known loci widely used in breeding. Obvious candidate SNP variants were identified in certain confidence intervals, such as the cloned gene Yr18 and the major locus on chromosome 2BL, despite a large extent of linkage disequilibrium. The number of causal SNP variants was refined using an independent validation panel and consideration of the estimated functional importance of each nucleotide polymorphism. Interestingly, four natural polymorphisms causing amino acid changes in the gene TraesCS2B01G513100 that encodes a serine/threonine protein kinase (STPK) were significantly involved in YR responses. Gene expression and mutation analysis confirmed that STPK played an important role in YR resistance. PCR markers were developed to identify the favourable TraesCS2B01G513100 haplotype for marker‐assisted breeding. These results demonstrate that high‐resolution SNP‐based GWAS enables the rapid identification of putative resistance genes and can be used to improve the efficiency of marker‐assisted selection in wheat disease resistance breeding.

Low temperature is a serious threat to the seed emergence of rice, which has become one of the main limiting factors affecting rice production in the world. It is of great significance to find the candidate genes controlling low-temperature tolerance during seed germination and study their functions for breeding new rice cultivars with immense low-temperature tolerance during seed germination. In the current experiment, 120 lines of the Cheongcheong Nagdong Double Haploid (CNDH) population were used for quantitative trait locus (QTL) analysis of low-temperature germinability. The results showed a significant difference in germination under low different temperature (LDT) (15 °C, 20 °C) conditions. In total, four QTLs were detected on chromosome 3, 6, and 8. A total of 41 genes were identified from all the four QTLs, among them, 25 genes were selected by gene function annotation and further screened through quantitative real-time polymerase chain reaction (qRT-PCR). Based on gene function annotation and level of expression under low-temperature, our study suggested the OsGPq3 gene as a candidate gene controlling viviparous germination, ABA and GA signaling under low-temperature. This study will provide a theoretical basis for marker-assisted breeding and lay the basis for further mining molecular mechanisms of low-temperature germination tolerance in rice.

After yield, quality is one of the most important aspects of rice breeding. Preference for rice quality varies among cultures and regions; therefore, rice breeders have to tailor the quality according to the preferences of local consumers. Rice quality assessment requires routine chemical analysis procedures. The advancement of molecular marker technology has revolutionized the strategy in breeding programs. The availability of rice genome sequences and the use of forward and reverse genetics approaches facilitate gene discovery and the deciphering of gene functions. A well-characterized gene is the basis for the development of functional markers, which play an important role in plant genotyping and, in particular, marker-assisted breeding. In addition, functional markers offer advantages that counteract the limitations of random DNA markers. Some functional markers have been applied in marker-assisted breeding programs and have successfully improved rice quality to meet local consumers' preferences. Although functional markers offer a plethora of advantages over random genetic markers, the development and application of functional markers should be conducted with care. The decreasing cost of sequencing will enable more functional markers for rice quality improvement to be developed, and application of these markers in rice quality breeding programs is highly anticipated.

The fruit of date palm trees are an important part of the diet for a large portion of the Middle East and North Africa. The fruit is consumed both fresh and dry and can be stored dry for extended periods of time. Date fruits vary significantly across hundreds of cultivars identified in the main regions of cultivation. Most dried date fruit are low in sucrose but high in glucose and fructose. However, high sucrose content is a distinctive feature of some date fruit and affects flavor as well as texture and water retention. To identify the genes controlling high sucrose content, we analyzed date fruit metabolomics for association with genotype data from 120 date fruits. We found significant association of dried date sucrose content and a genomic region that contains 3 tandem copies of the beta‐fructofuranosidase (invertase) gene in the reference Khalas genome, a low‐sucrose fruit. High‐sucrose cultivars including the popular Deglet Noor had a homozygous deletion of two of the 3 copies of the invertase gene. We show the deletion allele is derived when compared to the ancestral allele that retains all copies of the gene in 3 other species of Phoenix. The fact that 2 of the 3 tandem invertase copies are associated with dry fruit sucrose content will assist in better understanding the distinct roles of multiple date palm invertases in plant physiology. Identification of the recessive alleles associated with end‐point sucrose content in date fruit may be used in selective breeding in the future.

Society Impact Statement Until the 1970s, the majority of commercial strawberry varieties produced a single bloom of flowers. However, continuously flowering, everbearing strawberries are now routinely cultivated and use is increasing. Indeed, introgression of the everbearing flowering trait can lead to economic benefits for growers through the production of a continual crop from the same plant. Genetically guided improvement has the power to streamline everbearing generation. As such, the genetic markers reported here can help to identify everbearing individuals at an early time point in the breeding process. Furthermore, these markers can help to improve the predictions of progeny segregation ratios. Summary Previous work within the community led to the identification of a single dominant allele that controls the everbearing trait. However, frequent observations have indicated that crosses do not segregate in a Mendelian fashion, as would be expected for a trait controlled by a single dominant gene. Therefore, it was hypothesised that one or more unidentified epistatic alleles interact with the major gene. A genome‐wide association study (GWAS) was conducted on 587 June bearers and 207 everbearers to assess the genetic components associated with flowering habit. The segregation ratios of parental strawberry lines with known phenotypes were used to validate the identified alleles. Three loci including the known major FaPFRU locus and two epistatic modifiers were identified. These modifiers function as enhancers of the everbearing trait in individuals containing a single copy of the FaPFRU everbearing allele and appear to be functionally redundant. Principally, heterozygous individuals required the presence of two modifying alleles in order to allow expression of the everbearing trait. Inclusion of the epistatic alleles improved the prediction of everbearing segregation ratios; beyond that of a single allele model, however, a large proportion of the variation remained unexplained. Future work should identify the additional repressor and enhancer modifiers not identified here. Discovering the genetic components controlling the everbearing trait can enable genetic informed strawberry improvement. Until the 1970s, the majority of commercial strawberry varieties produced a single bloom of flowers. However, continuously flowering, everbearing strawberries are now routinely cultivated and use is increasing. Indeed, introgression of the everbearing flowering trait can lead to economic benefits for growers through the production of a continual crop from the same plant. Genetically guided improvement has the power to streamline everbearing generation. As such, the genetic markers reported here can help to identify everbearing individuals at an early time point in the breeding process. Furthermore, these markers can help to improve the predictions of progeny segregation ratios.

In this study, 71 durum wheat cultivars (Triticum durum Desf.), 22 emmer wheat (Triticum dicoccum L.) and 11 wild emmer (Triticum dicoccoides L.) genotypes were genetically characterized to determine the alleles associated with high cadmium (Cd) content. After genotypic characterization, 14 cultivars selected among all genotypes with low and high Cd content were phenotyped by a pot experiment to verify the genotypic data. Identification of 32 durum wheat, one emmer wheat and four wild emmer genotypes showed that they have alleles associated with high Cd content, while 68 genotypes of which 39 durum wheat, 21 emmer wheat and 7 wild emmer cultivars had alleles associated with low Cd content. Moreover, phenotypic data obtained from pot experiment were similar to the molecular data. To sum up, the marker successfully classified durum wheat cultivars into either high or low accumulators and these results can be safely used in breeding programs to improve new durum wheat cultivars with alleles associated with low Cd content. Due to routine use of phosphorus fertilizers in agricultural areas and other anthropogenic factors related to Cd toxicity, new durum wheat cultivars with low Cd content should be urgently developed for safe production of macaroni or other types of wheat products for human and animal consumption.

Grain shape is one of the key factors deciding the yield product and the market value as appearance quality in rice (Oryza sativa L.). The grain shape of japonica cultivars in Korea is quite monotonous because the selection pressure of rice breeding programs works in consideration of consumer preference. In this study, we identified QTLs associated with grain shape to improve the variety of grain shapes in Korean cultivars. QTL analysis revealed that eight QTLs related to five tested traits were detected on chromosomes 2, 5, and 10. Among them, three QTLs—qGL2 (33.9% of PEV for grain length), qGW5 (64.42% for grain width), and qGT10 (49.2% for grain thickness)—were regarded as the main effect QTLs. Using the three QTLs, an ideal QTL combination (qGL2P + qGW5P + qGT10B) could be constructed on the basis of the accumulated QTL effect without yield loss caused by the change in grain shape in the population. In addition, three promising lines with a slender grain type were selected as a breeding resource with a japonica genetic background based on the QTL combination. The application of QTLs detected in this study could improve the grain shape of japonica cultivars without any linkage drag or yield loss.

The increased occurrence and severity of drought stress have led to a high yield decline in rice in recent years in drought-affected areas. Drought research at the International Rice Research Institute (IRRI) over the past decade has concentrated on direct selection for grain yield under drought. This approach has led to the successful development and release of 17 high-yielding drought-tolerant rice varieties in South Asia, Southeast Asia, and Africa. In addition to this, 14 quantitative trait loci (QTLs) showing a large effect against high-yielding drought-susceptible popular varieties were identified using grain yield as a selection criterion. Six of these (qDTY1.1, qDTY2.2, qDTY3.1, qDTY3.2, qDTY6.1, and qDTY12.1) showed an effect against two or more high-yielding genetic backgrounds in both the lowland and upland ecosystem, indicating their usefulness in increasing the grain yield of rice under drought. The yield of popular rice varieties IR64 and Vandana has been successfully improved through a well-planned marker-assisted backcross breeding approach, and QTL introgression in several other popular varieties is in progress. The identification of large-effect QTLs for grain yield under drought and the higher yield increase under drought obtained through the use of these QTLs (which has not been reported in other cereals) indicate that rice, because of its continuous cultivation in two diverse ecosystems (upland, drought tolerant, and lowland, drought susceptible), has benefited from the existence of larger genetic variability than in other cereals. This can be successfully exploited using marker-assisted breeding.

Phytoextraction by high-Cd-accumulating rice lacking a functional OsHMA3 allele is promising for Cd removal from paddy soils. To increase rice Cd extraction efficiency, we developed a new high-Cd variety, TJN25-11. For this, we pyramided a nonfunctional OsHMA3 allele from a high-Cd variety, Jarjan, and two QTLs for increased shoot Cd concentrations, which were discovered in a mapping population derived from a high-Cd variety, Nepal 555, and a low-Cd variety, Tachisugata. In two Cd-contaminated paddy fields under drained aerobic soil conditions, TJN25-11 presented significantly higher Cd concentrations in the straw and panicles than the OsHMA3-deficient varieties TJTT8 and Cho-ko-koku. Among the varieties, TJN25-11 had a relatively high shoot biomass, resulting in the highest Cd accumulation in the shoots. The soil Cd decreased by approximately 20% after TJN25-11 growth. The amount of Cd that accumulated in the TJN25-11 aerial parts was much greater than the amount of Cd that decreased in the topsoil, suggesting that Cd was absorbed from deeper soil layers. Thus, we revealed the effects of QTL pyramiding on shoot Cd accumulation and Cd phytoextraction efficiency. Since TJN25-11 has favorable agronomic traits for compatibility with Japanese cultivation systems, this variety could be useful for Cd phytoextraction in Cd-contaminated paddy fields.