A pan‐genome and chromosome‐length reference genome of narrow‐leafed lupin (Lupinus angustifolius) reveals genomic diversity and insights into key industry and biological traits

The Plant Journal, Journal Year: 2022, Volume and Issue: 111(5), P. 1252 - 1266

Published: July 2, 2022

Narrow-leafed lupin (NLL; Lupinus angustifolius) is a key rotational crop for sustainable farming systems, whose grain high in protein content. It gluten-free, non-genetically modified, alternative source to soybean (Glycine max) and as such has gained interest human food ingredient. Here, we present chromosome-length reference genome the species pan-genome assembly comprising 55 NLL lines, including Australian European cultivars, breeding lines wild accessions. We core variable genes report on absence of essential mycorrhizal associated genes. The pan-genomes its close relative white (Lupinus albus) are compared. Furthermore, provide additional evidence supporting LaRAP2-7 alkaloid regulatory gene demonstrate underrepresented classical NLR disease resistance compared other sequenced legume species. genomic resources generated here coupled with previously RNA sequencing datasets new opportunities fast-track improvement.

Language: Английский

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Targeted mutagenesis with sequence‐specific nucleases for accelerated improvement of polyploid crops: Progress, challenges, and prospects

The Plant Genome, Journal Year: 2023, Volume and Issue: 16(2)

Published: Jan. 24, 2023

Many of the world's most important crops are polyploid. The presence more than two sets chromosomes within their nuclei and frequently aberrant reproductive biology in polyploids present obstacles to conventional breeding. a larger number homoeologous copies each gene makes random mutation breeding daunting task for polyploids. Genome editing has revolutionized improvement polyploid as multiple and/or alleles can be edited simultaneously while preserving key attributes elite cultivars. Most genome-editing platforms employ sequence-specific nucleases (SSNs) generate DNA double-stranded breaks at target gene. Such typically repaired via error-prone nonhomologous end-joining process, which often leads frame shift mutations, causing loss function. enhanced disease resistance, yield components, end-use quality crops. However, identification candidate targets, genotyping, requirement high mutagenesis efficiency remain bottlenecks targeted In this review, we will survey tremendous progress SSN-mediated crop improvement, discuss its challenges, identify optimizations needed sustain further progress.

Language: Английский

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GAEP: a comprehensive genome assembly evaluating pipeline

Journal of genetics and genomics/Journal of Genetics and Genomics, Journal Year: 2023, Volume and Issue: 50(10), P. 747 - 754

Published: May 26, 2023

With the rapid development of sequencing technologies, especially maturity third-generation there has been a significant increase in number and quality published genome assemblies. The emergence these high-quality genomes raised higher requirements for evaluation. Although numerous computational methods have developed to evaluate assembly from various perspectives, selective use evaluation can be arbitrary inconvenient fairly comparing quality. To address this issue, we Genome Assembly Evaluating Pipeline (GAEP), which provides comprehensive assessment pipeline evaluating multiple including continuity, completeness, correctness. Additionally, GAEP includes new functions detecting misassemblies redundancy, performs well our testing. is publicly available at https://github.com/zy-optimistic/GAEP under GPL3.0 License. GAEP, users quickly obtain accurate reliable results, facilitating comparison selection

Language: Английский

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Analysis of Phenotypic and Physiological Characteristics of Plant Height Difference in Alfalfa

Agronomy, Journal Year: 2023, Volume and Issue: 13(7), P. 1744 - 1744

Published: June 28, 2023

Cultivating new alfalfa (Medicago sativa L.) varieties with high yield and quality is of great significance for improving promoting the development grass livestock industry. Plant height an important indicator closely related to photosynthetic capacity, harvest index yield. However, underlying cause variation in among plants not clear. In this paper, we measured phenotypic traits, physiology endogenous hormone content tall- short-stalked materials analyzed external internal factors that caused difference plant alfalfa. We found traits showed significant differences, dwarf shortening main stem internode length. There were also some differences light physiological indicators contents between materials. Through correlation analysis, significantly correlated number internodes, diameter, average length, leaf–stem ratio, leaf area, Pn (net rate), Tr (transpiration upper SP (soluble protein), Suc (sucrose) content, middle Sta (starch) ZT (zeatin) IAA (indole-3-acetic acid). Further analysis Tr, LA played a direct role height, contributing most followed by IAA. Finally, starch had impact on through principal component analysis. These results provide insights into formation genetic improvement leguminous forages such as

Language: Английский

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Comparative Analysis of Chloroplast Pan-Genomes and Transcriptomics Reveals Cold Adaptation in Medicago sativa

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(3), P. 1776 - 1776

Published: Feb. 1, 2024

Alfalfa (

Language: Английский

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