Functional Markers for Precision Plant Breeding

Abstract

<jats:p>Advances in molecular biology including genomics, high-throughput sequencing, and genome editing enable increasingly faster and more precise cultivar development. Identifying genes and functional markers (FMs) that are highly associated with plant phenotypic variation is a grand challenge. Functional genomics approaches such as transcriptomics, targeting induced local lesions in genomes (TILLING), homologous recombinant (HR), association mapping, and allele mining are all strategies to identify FMs for breeding goals, such as agronomic traits and biotic and abiotic stress resistance. The advantage of FMs over other markers used in plant breeding is the close genomic association of an FM with a phenotype. Thereby, FMs may facilitate the direct selection of genes associated with phenotypic traits, which serves to increase selection efficiencies to develop varieties. Herein, we review the latest methods in FM development and how FMs are being used in precision breeding for agronomic and quality traits as well as in breeding for biotic and abiotic stress resistance using marker assisted selection (MAS) methods. In summary, this article describes the use of FMs in breeding for development of elite crop cultivars to enhance global food security goals.</jats:p>

The Genetic Basis of Tomato Aroma

“…This may not only lead to the identification of the causal genes controlling a trait, but also to the detection of the causal genetic variants underlying trait variation. Such variants, also called functional markers, are the best possible molecular markers for MAS, since they are functionally linked to the trait rather than genetically linked and their use as marker does not need validation in other populations, which is always required with genetically-linked markers [196]. (iv) The information on large effect aroma QTLs provided in this review can alo be used to improve the performance of genomic prediction models, since both geneticallylinked markers and in particular functional markers have been shown to significantly improve the prediction power of GP models compared to the use of random neutral markers [197].…”

Importance of Landraces in Cereal Breeding for Stress Tolerance

“…The availability of genome sequences of different species has made possible the development of functional markers to be used in breeding. For example, for one of the major blast resistance genes in rice, Pi54 , a PCR-based co-dominant molecular marker targeting an InDel identified in the exonic region of the gene, co-segregating with blast resistance, has been developed and used for routine deployment in MAS in breeding programs [ 156 , 157 ].…”

Control of Plant Viral Diseases by CRISPR/Cas9: Resistance Mechanisms, Strategies and Challenges in Food Crops

“…Resistance breeding should not depend on extreme molecular characterization of resistance gene alleles and the target a virulence (avr) determinant of a virus. In a practical sense, the successful deployment of a potential resistance gene into a crop depends more upon the identification of a positive phenotype, on the dissection of the phenotype, leading to the identification of genetic markers for marker-assisted selective breeding (MAS) and on an understanding of how the novel resistance will behave in different genetic backgrounds and under pathogen pressure in the field [ 44 ]. However, the focus is mainly on monogenic dominant resistance to bacterial and fungal pathogens, and the common mechanisms can also be employed in virus resistance.…”

“…Cas9 may disseminate these mutant viruses from plants and with multiple sgRNAs [ 26 ]. In addition to targeting or interfering with the viral genome to inhibit its infection, CRISPR/Cas9 can generate new viral variants as genome-editing by-products that speed up the evolution of the virus, causing the produced transgenic crops to lose their resistance capacity against these viruses [ 44 ]. These limitations are shortcomings of the CRISPR/Cas9 tool against some plant viruses.…”