Apple quality traits such as fruit texture, sugar content, and firmness retention during storage are key targets for breeders. Understanding the genetic control of fruit quality traits can enable the ...development of genetic markers, useful for marker-assisted breeding of new apple cultivars. We made use of over 260,000 single nucleotide polymorphisms (SNPs) genotyped across 1,054 apple accessions from Canada's Apple Biodiversity Collection to perform genome-wide association for 21 fruit quality and phenology traits. We identified two loci on chromosome 15 and 16 associated with phenolic content and a locus on chromosome 10 associated with softening. In addition, we determined that allelic variation at the NAC18.1 transcription factor was associated with numerous traits including harvest date, firmness at harvest, and firmness after storage. Our analyses suggest that NAC18.1 independently acts as a high level regulator of multiple ripening related traits and we propose a model for the allelic effects at NAC18.1 on apple ripening and softening.
Soybean is the world's leading source of vegetable protein and demand for its seed continues to grow. Breeders have successfully increased soybean yield, but the genetic architecture of yield and key ...agronomic traits is poorly understood. We developed a 40-mating soybean nested association mapping (NAM) population of 5,600 inbred lines that were characterized by single nucleotide polymorphism (SNP) markers and six agronomic traits in field trials in 22 environments. Analysis of the yield, agronomic, and SNP data revealed 23 significant marker-trait associations for yield, 19 for maturity, 15 for plant height, 17 for plant lodging, and 29 for seed mass. A higher frequency of estimated positive yield alleles was evident from elite founder parents than from exotic founders, although unique desirable alleles from the exotic group were identified, demonstrating the value of expanding the genetic base of US soybean breeding.
•The purple-leaved trait is governed by a single nuclear gene with dominant inheritance.•The candidate region that controls the purple-leaved trait was located within a 189.4 kb interval (between ...markers I-63 and I-64) on chromosome A03, containing 16 genes.•Within this intervalthe candidate gene BraA03g064730.3C, encoding NAD-dependent epimerase/dehydratase involved in anthocyanin metabolism, exhibited differential expression in plants with varied leaf colors.•There is a single-base substitution (G→T) in exon 1 in BraA03g064730.3C, resulting in an amino acid change from valine to phenylalanine..•qRT-PCR revealed that BraA03g064730.3C exhibited significantly different expression in S46P and S46G. we hypothesize that BraA03g064730.3C plays a positive regulatory role in the control of the purple-leaved trait.
Anthocyanins are water-soluble pigments widely found in plants and play an important role in plant stress resistance and the prevention of chronic diseases in humans. Purple non-heading Chinese cabbage, known for its rich anthocyanin content and significant nutritional and health benefits, is a focal point for enhancing the appearance quality of non-heading Chinese cabbage through breeding. In this study, an F2 population resulted from the hybridization of the purple-leaved parental line S46P with the green-leaved line S46G. Genetic analysis revealed a 3:1 ratio consistent with Mendelian inheritance, indicating that the purple-leaved trait is governed by a single nuclear gene with dominant inheritance. Using BSA-seq technology, the gene was initially mapped to a 3.41 Mb interval on chromosome A03. Subsequent positional cloning pinpointed the target gene between markers I-63 and I-64, spanning 189.4 kb. Within this interval, 16 candidate genes were predicted. Variant annotation identified three genes with coding region mutations with amino acid changes. Notably, the candidate gene BraA03g064730.3C, encoding NAD-dependent epimerase/dehydratase involved in anthocyanin metabolism, exhibited differential expression in plants with varied leaf colors. Map-based cloning and sanger-sequencing revealed a single-base substitution (G→T) in exon 1, resulting in the amino acid change from valine to phenylalanine. This SNP mutation is speculated to alter the function or expression of the BraA03g064730.3C gene, confirming its candidacy for controlling the purple-leaved trait in non-heading Chinese cabbage. Furthermore, the low-light treatment showed that changes in the expression of BraA03g064730.3C is correlated with anthocyanin content. This discovery establishes a foundation for delving into the molecular mechanisms of anthocyanin synthesis and offers theoretical support and gene source for breeding varieties with diverse leaf colors of non-heading Chinese cabbage.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Chromosomal inversions have the potential to play an important role in evolution by reducing recombination between favorable combinations of alleles. Until recently, however, most evidence for their ...likely importance derived from dipteran flies, whose giant larval salivary chromosomes aided early cytogenetic studies. The widespread application of new genomic technologies has revealed that inversions are ubiquitous across much of the plant and animal kingdoms. Here we review the rapidly accumulating literature on inversions in the plant kingdom and discuss what we have learned about their establishment and likely evolutionary role. We show that inversions are prevalent across a wide range of plant groups. We find that inversions are often associated with locally favored traits, as well as with traits that contribute to assortative mating, suggesting that they may be key to adaptation and speciation in the face of gene flow. We also discuss the role of inversions in sex chromosome formation, and explore possible parallels with inversion establishment on autosomes. The identification of inversion origins, as well as the causal variants within them, will advance our understanding of chromosomal evolution in plants.
Many important crops (e.g., tuber, root, and tree crops) are cross-pollinating. For these crops, no inbred lines are available for genetic study and breeding because they are self-incompatible, ...clonally propagated, or have a long generation time, making the identification of agronomically important genes difficult, particularly in crops with a complex autopolyploid genome. In this study, we developed a method, OutcrossSeq, for mapping agronomically important loci in outcrossing crops based on whole-genome low-coverage resequencing of a large genetic population, and designed three computation algorithms in OutcrossSeq for different types of outcrossing populations. We applied OutcrossSeq to a tuberous root crop (sweet potato, autopolyploid), a tree crop (walnut tree, highly heterozygous diploid), and hybrid crops (double-cross populations) to generate high-density genotype maps for the outcrossing populations, which enable precise identification of genomic loci underlying important agronomic traits. Candidate causative genes at these loci were detected based on functional clues. Taken together, our results indicate that OutcrossSeq is a robust and powerful method for identifying agronomically important genes in heterozygous species, including polyploids, in a cost-efficient way. The OutcrossSeq software and its instruction manual are available for downloading at www.xhhuanglab.cn/tool/OutcrossSeq.html.
The complexity inherent in outcrossing plants and autopolyploid plants makes genetic studies and molecular breeding rather difficult. A method, OutcrossSeq, is now developed for high-density genotyping, imputation and haplotyping in outcrossing plants. The tool will facilitate genetic mapping of agronomically important loci and help breeding selections in outcrossing crops.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
The rapid expansion of next‐generation sequencing has yielded a powerful array of tools to address fundamental biological questions at a scale that was inconceivable just a few years ago. Various ...genome‐partitioning strategies to sequence select subsets of the genome have emerged as powerful alternatives to whole‐genome sequencing in ecological and evolutionary genomic studies. High‐throughput targeted capture is one such strategy that involves the parallel enrichment of preselected genomic regions of interest. The growing use of targeted capture demonstrates its potential power to address a range of research questions, yet these approaches have yet to expand broadly across laboratories focused on evolutionary and ecological genomics. In part, the use of targeted capture has been hindered by the logistics of capture design and implementation in species without established reference genomes. Here we aim to (i) increase the accessibility of targeted capture to researchers working in nonmodel taxa by discussing capture methods that circumvent the need of a reference genome, (ii) highlight the evolutionary and ecological applications where this approach is emerging as a powerful sequencing strategy and (iii) discuss the future of targeted capture and other genome‐partitioning approaches in the light of the increasing accessibility of whole‐genome sequencing. Given the practical advantages and increasing feasibility of high‐throughput targeted capture, we anticipate an ongoing expansion of capture‐based approaches in evolutionary and ecological research, synergistic with an expansion of whole‐genome sequencing.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
Wheat is a crop of historical significance, as it marks the turning point of human civilization 10,000 years ago with its domestication. Due to the rapid increase in population, wheat production ...needs to be increased by 50% by 2050 and this growth will be mainly based on yield increases, as there is strong competition for scarce productive arable land from other sectors. This increasing demand can be further achieved using sustainable approaches including integrated disease pest management, adaption to warmer climates, less use of water resources and increased frequency of abiotic stress tolerances. Out of 200 diseases of wheat, 50 cause economic losses and are widely distributed. Each year, about 20% of wheat is lost due to diseases. Some major wheat diseases are rusts, smut, tan spot, spot blotch, fusarium head blight, common root rot, septoria blotch, powdery mildew, blast, and several viral, nematode, and bacterial diseases. These diseases badly impact the yield and cause mortality of the plants. This review focuses on important diseases of the wheat present in the United States, with comprehensive information of causal organism, economic damage, symptoms and host range, favorable conditions, and disease management strategies. Furthermore, major genetic and breeding efforts to control and manage these diseases are discussed. A detailed description of all the QTLs, genes reported and cloned for these diseases are provided in this review. This study will be of utmost importance to wheat breeding programs throughout the world to breed for resistance under changing environmental conditions.
Plant architectures is predominantly determined by branching pattern, internode elongation, phyllotaxis, shoot determinacy and reproductive organs. Domestication or improvement of this critical ...agronomic trait played an important role in the breakthrough of crop yield. Here, we identified a mutant with fasciated plant architecture, named fas, from an ethyl methanesulfonate (EMS) induced mutant population in cucumber. The mutant exhibited abnormal phyllotaxy, flattened main stem, increased number of floral organs, and significantly shorter and thicker fruits. However, the molecular mechanism conferring this pleiotropic effect remains unknown. Using a map-based cloning strategy, we isolated the gene CsaV3_3G045960, encoding a leucine-rich repeat receptor-like kinase, a putative direct homolog of the Arabidopsis CLAVATA1 protein referred to as CsCLV1. Endogenous hormone assays showed that IAA and GA3 levels in fas stems and ovaries were significantly reduced. Conformably, RNA-seq analysis showed that CsCLV1 regulates cucumber stem and ovary development by coordinating hormones and transcription factors. Our results contribute to the understanding of the function of CsCLV1 throughout the growth cycle, provide new evidence that the CLV signaling system is functionally conserved in Cucurbitaceae.
•Identification of a fasciated locu, fas, in cucumber.•fas encodes a leucine-rich repeat receptor-like protein kinase CLAVATA1.•CsCLV1 is required for stem and lateral organ morphogenesis development.•Differential expression of genes involved in hormones and SAM maintenance.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Chinese wheat landrace Youbailan has excellent resistance to powdery mildew caused by Blumeria graminis f. sp. tritici. In the present study, genetic analysis indicated that a recessive gene, ...tentatively designated pmYBL, was responsible for the powdery mildew resistance of Youbailan. pmYBL was located in the 695-to-715-Mb genomic region of chromosome 7BL, with 19 gene-linked single-nucleotide polymorphism (SNP) markers. It was flanked by SNP1-12 and SNP1-2 with genetic distances of 0.6 and 1.8 centimorgans, respectively. The disease reaction patterns of Youbailan and four cultivars (lines) carrying the powdery mildew (Pm) genes located on chromosome arm 7BL indicated that pmYBL may be allelic or closely linked to these genes. All of the SNP markers linked to pmYBL were diagnostic, indicating that these markers will be useful for pyramiding pmYBL using marker-assisted selection.
Summary
Next‐generation whole‐genome shotgun assemblies of complex genomes are highly useful, but fail to link nearby sequence contigs with each other or provide a linear order of contigs along ...individual chromosomes. Here, we introduce a strategy based on sequencing progeny of a segregating population that allows de novo production of a genetically anchored linear assembly of the gene space of an organism. We demonstrate the power of the approach by reconstructing the chromosomal organization of the gene space of barley, a large, complex and highly repetitive 5.1 Gb genome. We evaluate the robustness of the new assembly by comparison to a recently released physical and genetic framework of the barley genome, and to various genetically ordered sequence‐based genotypic datasets. The method is independent of the need for any prior sequence resources, and will enable rapid and cost‐efficient establishment of powerful genomic information for many species.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
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