Genomic Approaches of Crops Genetic Diversity

Way before the advances of crops genomic biotechnologies, pedigree and geographical distribution analyses of plants were used for the evaluation of genetic diversities [1] and crops were profiled using only morphology and phenotypic aspects [2].

For thousands of years, crop genetic diversity (the variation of the genes within a crop species), was the only result of domestication and practices of crop production with relatively few and genetically similar high-yielding cultivars [3]. Nowadays, and since food security and availability are threatened by the incapability of crops to quickly adapt to changing environmental conditions and increasing food demand [4], many efforts were made to enhance the genetic diversity of elite breeding pools using mutants, landraces, and ⁄ or wild species closely related to the cultivated crop.

The development of the molecular marker techniques has been useful for genotyping analysis [5], determination of phylogenetic relationships, population structure, map-based cloning, QTL (Quantitative Trait Loci) mapping and MAS (Marker Assisted Selection). But these techniques do not seem very suitable for measuring the adaptive genetic diversity of crops [6]. Therefore, diversity analysis should be based on functional genes or whole-genome sequences.

From the early 90’s and till today, only few plants and crops genomes have been sequenced [7] and are presented in genome-based databases that incorporate many levels and types of information such as the QTLs, mutants, physical maps, expression data, markers, and genetic diversity. In fact, the decreasing quality of genome sequences makes the organization of the data very difficult. The more fragmented is the genome; the more difficult is the creation of a useful database with exploitable information.

In the last decade, the application of NGS (Next-Generation Sequencing) technologies started to be widely applied for the resequencing of crop species that have a complete reference genome sequence. It was mainly used for finding SNPs suitable as DNA markers [8], examination of selection patterns either in advanced populations or during domestication [9,10], or finding functional alleles [11]. In fact, the objective for re-sequencing genomes within a species is to understand the molecular basis for “phenotype–genotype” relationships.

However, de novo assembly (not requiring a reference genome) using NGS with short-read lengths seems not very suitable for crops genome sequencing due to the high complexity of most plant genomes as a result of extensive duplication and the presence of repeat sequences [12].

While Genome-wide SNP genotyping is a powerful tool for evolutionary studies and association mapping [13], communitydeveloped SNP panels present limited utility in wider sets of germ plasm. But, genotyping by sequencing will overcome these limitations and afford many more polymorphic markers [14].

Diversity panels of genotypes presented in a particular species with reference genome sequences using NGS technologies will provide a platform for understanding existing genetic diversity, phenotypes with their related genes and exploiting natural genetic diversity to help develop greater genotypes. In order to do this effectively, extensive phenotypic data must be collected for the diversity panels and combined with re-sequencing data [15].

It is important to know that collecting phenotypic data remains the most complicated task for effective use of genomics technologies in advanced plant improvement. Phenotypic traits need an experienced eye and a skilled hand to score them effectively and consistently. Therefore, phenomics (mass collection of phenotypes) has not kept pace as in genomics and nowadays few people are being trained to collect relevant phenotypes [16].

Engineers and plant scientists must create new platforms to rapidly and accurately collect phenotypes on thousands of plants at a time before combining it to genomic approaches.

Improvements are being made, but equal advances in phenomics and genomics are needed in order to meet the world challenges on food security and availability.