Abstract
Simple SummaryHarnessing the natural and induced diversity existing in plant genetic resources is fundamental for building future crops more sober in fertilizers, water, and pesticides that can cope with climate instability while yielding healthier and more nutritious products. The essence of plant breeding is to combine favorable traits in crossing parental varieties to select novel performing associations amongst the progenies. These associations are the product of recombination between the parental chromosomes occurring during meiosis, mainly by a reciprocal DNA exchange called Cross Over (CO). However, recombination does not occur randomly along the chromosomes, and COs are limited in number often hampering the desired associations of favorable traits. This review surveys the recent advances in methods for achieving a stimulation and/or a redistribution of meiotic COs along the parental chromosomes and targeting COs specifically at desired chromosomal sites.Reciprocal (cross-overs = COs) and non-reciprocal (gene conversion) DNA exchanges between the parental chromosomes (the homologs) during meiotic recombination are, together with mutation, the drivers for the evolution and adaptation of species. In plant breeding, recombination combines alleles from genetically diverse accessions to generate new haplotypes on which selection can act. In recent years, a spectacular progress has been accomplished in the understanding of the mechanisms underlying meiotic recombination in both model and crop plants as well as in the modulation of meiotic recombination using different strategies. The latter includes the stimulation and redistribution of COs by either modifying environmental conditions (e.g., T°), harnessing particular genomic situations (e.g., triploidy in Brassicaceae), or inactivating/over-expressing meiotic genes, notably some involved in the DNA double-strand break (DSB) repair pathways. These tools could be particularly useful for shuffling diversity in pre-breeding generations. Furthermore, thanks to the site-specific properties of genome editing technologies the targeting of meiotic recombination at specific chromosomal regions nowadays appears an attainable goal. Directing COs at desired chromosomal positions would allow breaking linkage situations existing between favorable and unfavorable alleles, the so-called linkage drag, and accelerate genetic gain. This review surveys the recent achievements in the manipulation of meiotic recombination in plants that could be integrated into breeding schemes to meet the challenges of deploying crops that are more resilient to climate instability, resistant to pathogens and pests, and sparing in their input requirements.
Highlights
In order to tackle the major challenges faced by agriculture in the decades, plant breeding shall contribute by building novel crops resilient to climate change, resistant to pathogen and pest outbreaks, more resource-use efficient, and optimizing beneficial biological interactions
Experimental evidence that epigenetic factors influence recombination has been provided by analysis of double-strand break (DSB) hot spots (HS) and CO sites in mutants of genes involved in the maintenance of CG (MET1) and non-CG (CMT3) DNA methylations or imposition of repressive H3K9me2 marks (H3K9 methyltransferase genes KYP/SUVH4 SUVH5 SUVH6) [39,40,41,42]
AtSPO11-1–dependent meiocyte sRNAs enrichment at meiotic recombination associated DNA Motifs (CTT-repeat motif associated with genic regions and A-rich motif associated with gene promoters) suggest that AtSPO11-1–dependent sRNAs tend to be associated with the open chromatin structure, which might favor meiotic recombination HS, indicating a putative role of sRNAs in meiotic recombination. Taken together these results show that changes in meiotic recombination distribution, albeit moderate, can be expected from the inactivation of genes involved in the maintenance of CG and non-CG DNA methylation in plants
Summary
In order to tackle the major challenges faced by agriculture in the decades, plant breeding shall contribute by building novel crops resilient to climate change, resistant to pathogen and pest outbreaks, more resource-use efficient, and optimizing beneficial biological interactions. Shuffling can be hampered when favorable genes/alleles reside in chromosomal regions that are not or poorly amenable to recombination. This holds true for chromosomal regions exhibiting high interhomolog sequence divergence or structural variation in crosses. These divergent regions may contain important genes like some contributing to the dispensable genome, i.e., existing in only a subset of accessions, that represents a crucial gene reservoir for adaptation of crops to global change. Importance of the dispensable genome has recently been illustrated in rice by the isolation of genes underlying crucial adaptive mechanisms (e.g., submergence survival and avoidance, phosphorus uptake, fungal pathogen resistance) [1,2]. Gaining a better understanding of the mechanisms underlying meiotic recombination and developing tools for its modulation and targeting are of primary importance for improving plant breeding efficiency and accuracy
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