Innovative transcriptome‐based genotyping highlights environmentally responsive genes for phenology, growth and yield in a non‐model grain legume

Abstract

The narrow-leafed lupin, Lupinus angustifolius L., is a grain legume crop, cultivated both as a green manure and as a source of protein for animal feed and human food production. During its domestication process, numerous agronomic traits were improved, however, only two trait-related genes were identified hitherto, both by linkage mapping. Genome-wide association studies (GWAS), exploiting genomic sequencing, did not select any novel candidate gene. In the present study, an innovative method of 3 0-end reduced representation transcriptomic profiling, a massive analysis of cDNA ends, has been used for genotyping of 126 L. angustifolius lines surveyed by field phenotyping. Significant genotype × environment interactions were identified for all phenology and yield traits analysed. Principal component analysis of population structure evidenced European domestication bottlenecks, visualized by clustering of breeding materials and cultivars. GWAS provided contribution towards deciphering vernalization pathway in legumes, and, apart from highlighting known domestication loci (Ku/Julius and mol), designated novel candidate genes for L. angustifolius traits. Early phenology was associated with genes from vernalization, cold-responsiveness and phosphatidylinositol signalling pathways whereas high yield with genes controlling photosynthesis performance and abiotic stress (drought or heat) tolerance. PCR-based toolbox was developed and validated to enable tracking desired alleles in marker-assisted selection. Narrow-leafed lupin was genotyped with an innovative method of transcriptome profiling and phenotyped for phenology, growth and yield traits in field. Early phenology was found associated with genes from cold-response, vernalization and phosphatidylinositol signalling pathways, Piotr Plewi nski and Michał Książkiewicz contributed equally to the manuscript.

Genomic resources for lupins are coming of age

“…Similarly, genetic maps developed in yellow lupin and quantitative trait locus (QTL) analysis for flowering time and anthracnose resistance have identified candidate genes for these traits (Iqbal et al, 2019; Lichtin et al, 2020). More recently, massive analysis of cDNA ends (MACE) was employed for 126 NLL lines surveyed in the field for several agronomic traits to conduct a genome wide association study (GWAS) to identify genes associated with these traits (Plewinski et al, 2020). Strong marker trait associations were identified for the start and end to flowering, maturity, plant height, yield and total grain weight, where the deletion in the major flowering time locus LanFtc1 (Taylor et al, 2019) was strongly associated with both the start and end to flowering as well as maturity (Plewinski et al, 2020).…”

“…More recently, massive analysis of cDNA ends (MACE) was employed for 126 NLL lines surveyed in the field for several agronomic traits to conduct a genome wide association study (GWAS) to identify genes associated with these traits (Plewinski et al, 2020). Strong marker trait associations were identified for the start and end to flowering, maturity, plant height, yield and total grain weight, where the deletion in the major flowering time locus LanFtc1 (Taylor et al, 2019) was strongly associated with both the start and end to flowering as well as maturity (Plewinski et al, 2020). The MACE technique was also used for expression QTL mapping in NLL, constituting the first e‐QTL survey in lupins (Plewinski et al, 2019).…”

Development of PCR-based markers and whole-genome selection model for anthracnose resistance in white lupin (Lupinus albus L.)

“…A valid alternative analysis was genome-wide association mapping (GWAS), which can be used to score the association between thousands of SNP markers and the desired t r a i t . T h u s , G W A S w a s r e c e n t l y e x p l o i t e d i n L. angustifolius, highlighting novel candidate genes for phenology, growth, and yield traits (Plewiński et al 2020). However, it was shown that GWAS can lead to false associations if the trait of interest is present in a very small proportion (< 5%) of the population (Sonah et al 2015).…”

Progress of Genomics-Driven Approaches for Sustaining Underutilized Legume Crops in the Post-Genomic Era

“…Due to the unprecedented advances in NGS technology, an increasing repertoire of HTP markers in several underutilized legumes have helped to identify loci associated with aspects of complex trait architecture. GWAS has been assisted by the subsequent availability of genome-wide SNP markers for various traits, including phenological traits, quality/nutritional traits, biotic and abiotic stresses, and yield and yield-related traits, in many underutilized legumes ( Plewiński et al, 2020 ). In narrow-leafed lupin, a GWAS incorporating massive analysis of cDNA ends (MACE) markers in 126 gentoypes uncovered significant MTAs related to flower initiation, maturity, plant height, and yield traits ( Plewiński et al, 2020 ).…”

“…GWAS has been assisted by the subsequent availability of genome-wide SNP markers for various traits, including phenological traits, quality/nutritional traits, biotic and abiotic stresses, and yield and yield-related traits, in many underutilized legumes ( Plewiński et al, 2020 ). In narrow-leafed lupin, a GWAS incorporating massive analysis of cDNA ends (MACE) markers in 126 gentoypes uncovered significant MTAs related to flower initiation, maturity, plant height, and yield traits ( Plewiński et al, 2020 ). The underlying candidate genes were Lup019134, Lup015264, Lup021911, and Lup021909 for flower initiation, Lup015264 and Lup004734 for maturity, Medtr1g030750 for plant height, and Lup021835 and Lup022535 for yield traits ( Plewiński et al, 2020 ).…”