Transcriptome Resources Paving the Way for Lupin Crop Improvement

Kamphuis, Lars G.; Foley, Rhonda C.; Frick, Karen M.; Garg, Gagan; Singh, Karam B.

doi:10.1007/978-3-030-21270-4_5

Cited by 3 publications

(3 citation statements)

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“…To this end a range of genetic and genomic resources have been developed for NLL in recent years. These include the generation of bacterial artificial chromosome (BAC) libraries (Gao et al., 2011; Kasprzak et al., 2006), transcriptome datasets (reviewed in Kamphuis et al., 2020), cytogenetic maps (Bielski et al., 2020) and various genetic maps. In addition, a survey genome sequence was generated in 2013 for NLL (Yang et al., 2013), followed by the first comprehensive draft genome sequence coupled with a dense reference genetic map for the species (Hane et al., 2017).…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2022

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

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Section: Introductionmentioning

confidence: 99%

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

et al. 2022

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“…Co-expression studies with LDC/CAO in lupin (and LDC in S. flavescens ) have identified a growing number of candidate genes involved in QA accumulation in as yet unknown ways. The candidate genes include transcription factors, transporters, and a range of potential genes likely involved in metabolite modification ( Han et al, 2015 ; Yang et al, 2017 ; Kroc et al, 2019 ; Plewiński et al, 2019 ; Kamphuis et al, 2020 ). For candidate genes identified in lupin, we have demonstrated that a mirabait transcript capture ( Chevreux et al, 2004 ) and assembly strategy is an efficient way to use existing resources to obtain transcripts for candidate genes.…”

Section: Discussionmentioning

confidence: 99%

Analysis of Genetic Diversity in the Traditional Chinese Medicine Plant ‘Kushen’ (Sophora flavescens Ait.)

et al. 2021

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Kushen root, from the woody legume Sophora flavescens, is a traditional Chinese medicine that is a key ingredient in several promising cancer treatments. This activity is attributed in part to two quinolizidine alkaloids (QAs), oxymatrine and matrine, that have a variety of therapeutic activities in vitro. Genetic selection is needed to adapt S. flavescens for cultivation and to improve productivity and product quality. Genetic diversity of S. flavescens was investigated using genotyping-by-sequencing (GBS) on 85 plants grown from seeds collected from 9 provinces of China. DArTSeq provided over 10,000 single nucleotide polymorphism (SNP) markers, 1636 of which were used in phylogenetic analysis to reveal clear regional differences for S. flavescens. One accession from each region was selected for PCR-sequencing to identify gene-specific SNPs in the first two QA pathway genes, lysine decarboxylase (LDC) and copper amine oxidase (CAO). To obtain SfCAO sequence for primer design we used a targeted transcript capture and assembly strategy using publicly available RNA sequencing data. Partial gene sequence analysis of SfCAO revealed two recently duplicated genes, SfCAO1 and SfCAO2, in contrast to the single gene found in the QA-producing legume Lupinus angustifolius. We demonstrate high efficiency converting SNPs to Kompetitive Allele Specific PCR (KASP) markers developing 27 new KASP markers, 17 from DArTSeq data, 7 for SfLDC, and 3 for SfCAO1. To complement this genetic diversity analysis a field trial site has been established in South Australia, providing access to diverse S. flavescens material for morphological, transcriptomic, and QA metabolite analysis. Analysis of dissected flower buds revealed that anthesis occurs before buds fully open suggesting a potential for S. flavescens to be an inbreeding species, however this is not supported by the relatively high level of heterozygosity observed. Two plants from the field trial site were analysed by quantitative real-time PCR and levels of matrine and oxymatrine were assessed in a variety of tissues. We are now in a strong position to select diverse plants for crosses to accelerate the process of genetic selection needed to adapt kushen to cultivation and improve productivity and product quality.

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“…These EST datasets were predominantly used to convert expressed sequences into gene‐based molecular markers. This was achieved through identifying either sequence or length‐based polymorphisms between expressed sequence reads of different lupin lines and converting these into polymerase chain reaction (PCR)‐based molecular markers (reviewed in detail in Kamphuis et al, 2020). They have been successfully employed to construct the first genetic maps in white lupin ( L. albus ) (Croxford et al, 2008; Phan et al, 2007) and yellow lupin ( L. luteus ) (Iqbal et al, 2019; Lichtin et al, 2020) as well as improve the density of genetic maps in narrow‐leafed lupin (NLL) (Fischer et al, 2015; Nelson et al, 2006, 2010).…”

Section: Overview Of Lupin Transcriptome Resources and Their Use In Prebreeding/breeding Activitiesmentioning

confidence: 99%

Genomic resources for lupins are coming of age

et al. 2021

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Lupins are underutilised pulse crops subject to increasing interest for human consumption of the high‐protein grain. They are also valued as a source of animal nutrition and make an excellent break crop in agricultural production systems. Like other orphan legumes, the genomic revolution has made it cost‐effective to also apply modern genetic and genomic approaches in lupins. These have predominantly been conducted in the two major domesticated lupin species, namely, narrow‐leafed lupin (NLL; Lupinus angustifolius) and white lupin (Lupinus albus), with transcriptome studies also emerging in other domesticated and undomesticated species. This review provides an overview of the current lupin genomic resources developed including two reference genomes for NLL and white lupin, several transcriptome resources and the development of pan‐genomes for NLL and white lupin, and describes how these offer great potential to increase grain yield and quality for these recently domesticated pulse crops. Furthermore, we highlight the importance of lupins to further our understanding of many aspects of fundamental legume biology. Combined, this will aid breeders and growers to improve lupin crops to help meet the increasing demand for plant protein in more sustainable cropping systems.

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Transcriptome Resources Paving the Way for Lupin Crop Improvement

Cited by 3 publications

References 47 publications

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

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

Analysis of Genetic Diversity in the Traditional Chinese Medicine Plant ‘Kushen’ (Sophora flavescens Ait.)

Genomic resources for lupins are coming of age

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