Next generation sequencing (NGS) technologies are being used to generate whole genome sequences for a wide range of crop species. When combined with precise phenotyping methods, these technologies provide a powerful and rapid tool for identifying the genetic basis of agriculturally important traits and for predicting the breeding value of individuals in a plant breeding population. Here we summarize current trends and future prospects for utilizing NGS-based technologies to develop crops with improved trait performance and increase the efficiency of modern plant breeding. It is our hope that the application of NGS technologies to plant breeding will help us to meet the challenge of feeding a growing world population.

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Harvesting the promising fruits of genomics: Applying genome sequencing technologies to crop breeding

Pollen development is a critical step in plant development that is needed for successful breeding and seed formation. Manipulation of male fertility has proved a useful trait for hybrid breeding and increased crop yield. However, although there is a good understanding developing of the molecular mechanisms of anther and pollen anther development in model species, such as Arabidopsis and rice, little is known about the equivalent processes in important crops. Nevertheless the onset of increased genomic information and genetic tools is facilitating translation of information from the models to crops, such as barley and wheat; this will enable increased understanding and manipulation of these pathways for agricultural improvement.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/jipb.12425

Anther and pollen development: A conserved developmental pathway.

Improving wheat to remove coeliac epitopes but retain functionality.

Mutagenesis is an important tool in crop improvement. However, the hexaploid genome of wheat (Triticum aestivum L.) presents problems in identifying desirable genetic changes based on phenotypic screening due to gene redundancy. TILLING (Targeting Induced Local Lesions IN Genomes), a powerful reverse genetic strategy that allows the detection of induced point mutations in individuals of the mutagenized populations, can address the major challenge of linking sequence information to the biological function of genes and can also identify novel variation for crop breeding. Wheat is especially well-suited for TILLING due to the high mutation densities tolerated by polyploids. However, only a few wheat TILLING populations are currently available in the world, which is far from satisfying the requirement of researchers and breeders in different growing environments. In addition, current TILLING screening protocols require costly fluorescence detection systems, limiting their use, especially in developing countries. We developed a new TILLING resource comprising 2610 M(2) mutants in a common wheat cultivar 'Jinmai 47'. Numerous phenotypes with altered morphological and agronomic traits were observed from the M(2) and M(3) lines in the field. To simplify the procedure and decrease costs, we use unlabeled primers and either non-denaturing polyacrylamide gels or agarose gels for mutation detection. The value of this new resource was tested using PCR with RAPD and Intron-spliced junction (ISJ) primers, and also TILLING in three selected candidate genes, in 300 and 512 mutant lines, revealing high mutation densities of 1/34 kb by RAPD/ISJ analysis and 1/47 kb by TILLING. In total, 31 novel alleles were identified in the 3 targeted genes and confirmed by sequencing. The results indicate that this mutant population represents a useful resource for the wheat research community. We hope that the use of this reverse genetics resource will provide novel allelic diversity for wheat improvement and functional genomics.

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Development and characterization of a new TILLING population of common bread wheat (Triticum aestivum L.).

Next-generation sequencing (NGS)-based bulked-segregant analysis (BSA) approaches have been proven successful for rapidly mapping genes in plant species However, most such methods are based on mutants and usually only one gene controlling the mutant phenotype is identified In this study, NGS-based BSA was employed to map simultaneously two qualitative genes controlling cotyledon color of seed in soybean Yellow-cotyledon (YC) and green-cotyledon (GC) bulks from progenies of a biparental population (Zhonghuang30  Jiyu102) were sequenced The SNP-index of each SNP locus in YC and GC bulks was calculated and Δ(SNP-index) was used to identify two genomic regions on chromosomes 1 and 11 harboring respectively loci qCC1 and qCC2 These two BSA-seq-derived loci were further validated with SSR markers and fine-mapped qCC1 was mapped to a 307-kb region containing four annotated genes and qCC2 was mapped to a 677-kb region with nine genes These two regions contained respectively genes D1 and D2, which had previously been identified by homology-based cloning as being associated with cotyledon color Sequence analysis of the NGS data also identified a frameshift deletion in the coding region of D1 These results suggested that BSA-seq could accelerate the mapping of loci controlling qualitative traits, even if a trait is controlled by more than one locus

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Next-Generation Sequencing from Bulked-Segregant Analysis Accelerates the Simultaneous Identification of Two Qualitative Genes in Soybean

Structural characterization and antioxidant activity of Polygonatum sibiricum polysaccharides.

Vernalization is one of the most important traits for the adaptability of wheat; detecting variation in genes regulating the response of wheat to vernalization is of importance for classifying winter phenotypes. Ecotilling is a high throughput reverse genetics approach for detecting single nucleotide polymorphisms (SNPs) in the genes of a natural population. To simplify methodology and decrease costs, a modified Ecotilling method based on agarose gel electrophoresis was used to discover the occurrence of SNPs in the wheat vernalization gene VRN-A1 in a natural population of 106 accessions of hexaploid wheat varieties and their association with the winter/spring phenotype. Based on the SNPs detected, these accessions fell into three haplotypes, namely, 'A', 'B' and 'C', each with five, six, and three variations, respectively. The winter phenotype was mainly determined by haplotype 'A' and 'B', while the spring phenotype was mainly determined by haplotype 'C'. After sequence confirmation, three SNPs ('A/-', in the fourth intron; '-/A', in the sixth intron; 'T/C', in the seventh exon) were associated with wheat vernalization and another three mutations ('G/T' in the second intron; 'T/C' in the fourth exon; 'CA/--', in the fourth intron) had no identified effect. Therefore, Ecotilling with detection of DNA fragments by agarose gel electrophoresis can be used as an efficient method for detecting SNPs in genes of polyploidy materials, such as wheat.

/pdf/detection-of-snps-in-the-vrn-a1-gene-of-common-wheat-1qtuh0inju.pdf

Detection of SNPs in the VRN-A1 gene of common wheat (Triticum aestivum L.) by a modified Ecotilling method using agarose gel electrophoresis.

Rhizomes of the Polygonatum species are well-known in traditional Chinese medicine. The 2020 edition of Chinese Pharmacopoeia includes three different species that possess different pharmacological effects. Due to the lack of standardized discriminant compounds there has often been inadvertently incorrect prescriptions given for these medicines, resulting in serious consequences. Therefore, it is critical to accurately distinguish these herbal Polygonatum species. For this study, UPLC-Q-TOF-MS/MS based metabolomics was employed for the first time to discriminate between three Polygonatum species. Partial least squares discriminant analysis (PLS-DA) models were utilized to select the potential candidate discriminant compounds, after which MS/MS fragmentation patterns were used to identify them. Meanwhile, metabolic correlations were identified using the R language package corrplot, and the distribution of various metabolites was analyzed by box plot and the Z-score graph. As a result, we found that adenosine, sucrose, and pyroglutamic acid were suitable for the identification of different Polygonatum species. In conclusion, this study articulates how various herbal Polygonatum species might be more accurately and efficiently distinguished.

Metabolomics Study of Different Germplasm Resources for Three Polygonatum Species Using UPLC-Q-TOF-MS/MS

Abstract Ziziphus spinosa (Bunge) H.H. Hu ex F.H. Chen is a woody plant species of the family Rhamnaceae (order Rhamnales) that possesses high nutritional and medicinal value. Predicting the effects of climate change on the distribution of Z. spinosa is of great significance for the investigation, protection, and exploitation of this germplasm resource. For this study, optimized maximum entropy models were employed to predict the distribution patterns and changes of its present (1970–2000) and future (2050s, 2070s, and 2090s) potential suitable regions in China under multiple climate scenarios (SSP1‐2.6, SSP2‐4.5, SSP3‐7.0 & SSP5‐8.5). The results revealed that the total area of the present potential suitable region for Z. spinosa is 162.60 × 104 km2, which accounts for 16.94% of China's territory. Within this area, the regions having low, medium, and high suitability were 80.14 × 104 km2, 81.50 × 104 km2, and 0.96 × 104 km2, respectively, with the high suitability regions being distributed primarily in Shanxi, Hebei, and Beijing Provinces. Except for SSP‐1‐2.6‐2070s, SSP‐5‐8.5‐2070s, and SSP‐5‐8.5‐2090s, the suitable areas for Z. spinosa in the future increased to different degrees. Meanwhile, considering the distribution of Z. spinosa during different periods and under different climate scenarios, our study predicted that the low impact areas of Z. spinosa were mainly restricted to Shanxi, Shaanxi, Ningxia, Gansu, Liaoning, Inner Mongolia, and Jilin Provinces. The results of core distributional shifts showed that, except for SSP1‐2.6, the center of the potential suitable region of Z. spinosa exhibited a trend of gradually shifting to the northwest.

https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/ece3.8629

Shi-Qiang Wang

Papers

Development and characterization of a new TILLING population of common bread wheat (Triticum aestivum L.).

Structural characterization and antioxidant activity of Polygonatum sibiricum polysaccharides.

Detection of SNPs in the VRN-A1 gene of common wheat (Triticum aestivum L.) by a modified Ecotilling method using agarose gel electrophoresis.

Metabolomics Study of Different Germplasm Resources for Three Polygonatum Species Using UPLC-Q-TOF-MS/MS

Predicting potential distribution of Ziziphus spinosa (Bunge) H.H. Hu ex F.H. Chen in China under climate change scenarios