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Transcriptome-Wide Genetic Variations in the Legume Genus Leucaena for Fingerprinting and Breeding
Journal article   Open access   Peer reviewed

Transcriptome-Wide Genetic Variations in the Legume Genus Leucaena for Fingerprinting and Breeding

Yong Han, Alexander Abair, Julian van der Zanden, Madhugiri Nageswara-Rao, Saipriyaa Vasan, Roopali Bhoite, Marieclaire Castello, Donovan Bailey, Clinton Revell, Chengdao Li, …
Agronomy (Basel), Vol.14(7), 1519
2024
DOI: https://doi.org/10.3390/agronomy14071519
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Published1.75 MBDownloadView
CC BY V4.0,  Open Access

Abstract

Breeding Diploids DNA fingerprinting Flowering Gene frequency Gene sequencing Genetic diversity Genetic fingerprinting Genetic variance Genetics Genome-wide association studies Genomes Genomics Genotyping Hybridization Hybrids Legumes Leucaena Livestock Nucleotide sequence Nucleotides Phylogenetics Plant breeding Population genetics Population studies Ribonucleic acid Ribosomal DNA RNA Single-nucleotide polymorphism Sterility Transcriptomes
Leucaena is a versatile legume shrub/tree used as tropical livestock forage and in timber industries, but it is considered a high environmental weed risk due to its prolific seed production and broad environmental adaptation. Interspecific crossings between Leucaena species have been used to create non-flowering or sterile triploids that can display reduced weediness and other desirable traits for broad use in forest and agricultural settings. However, assessing the success of the hybridisation process before evaluating the sterility of putative hybrids in the target environment is advisable. Here, RNA sequencing was used to develop breeding markers for hybrid parental identification in Leucaena. RNA-seq was carried out on 20 diploid and one tetraploid Leucaena taxa, and transcriptome-wide unique genetic variants were identified relative to a L. trichandra draft genome. Over 16 million single-nucleotide polymorphisms (SNPs) and 0.8 million insertions and deletions (indels) were mapped. These sequence variations can differentiate all species of Leucaena from one another, and a core set of about 75,000 variants can be genetically mapped and transformed into genotyping arrays/chips for the conduction of population genetics, diversity assessment, and genome-wide association studies in Leucaena. For genetic fingerprinting, more than 1500 variants with even allele frequencies (0.4–0.6) among all species were filtered out for marker development and testing in planta. Notably, SNPs were preferable for future testing as they were more accurate and displayed higher transferability within the genus than indels. Hybridity testing of ca. 3300 putative progenies using SNP markers was also more reliable and highly consistent with the field observations. The developed markers pave the way for rapid, accurate, and cost-effective diversity assessments, variety identification and breeding selection in Leucaena.

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Source: InCites

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Collaboration types
Domestic collaboration
International collaboration
Citation topics
3 Agriculture, Environment & Ecology
3.4 Crop Science
3.4.96 QTL
Web Of Science research areas
Agronomy
Plant Sciences
ESI research areas
Agricultural Sciences
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