Twenty Years of Leptosphaeria maculans Population Survey in France Suggests Pyramiding Rlm3 and Rlm7 in Rapeseed Is a Risky Resistance Management Strategy.

Strategies for plant resistance gene deployment aim to preserve their durability to highly adaptable fungal pathogens. While the pyramiding of resistance genes is often proposed as an effective way to increase their durability, molecular mechanisms by which the pathogen can overcome the resistance also are important aspects to take into account. Here, we report a counterexample where pyramiding of two resistance genes of Brassica napus, Rlm3 and Rlm7, matching the Leptosphaeria maculans avirulence genes AvrLm3 and AvrLm4-7, respectively, favored the selection of double-virulent isolates. We previously demonstrated that the presence of a functional AvrLm4-7 gene in an isolate masks the Rlm3-AvrLm3 recognition. Rlm7 was massively deployed in France since 2004. L. maculans populations were surveyed on a large scale (>7,600 isolates) over a period of 20 years, and resistance gene deployment at the regional scale was determined. Mutations in isolates overcoming both resistance genes were analyzed. All data indicated that the simultaneous success of Rlm7, the deployment of varieties pyramiding Rlm3 and Rlm7, along with the decrease in areas cultivated with Rlm3 only, contributed to the success of virulent isolates toward Rlm7, and more recently to both Rlm3 and Rlm7. Experimental field assays proved that resistance gene alternation was a better strategy compared with pyramiding in this context. Our study also illustrated an unusually high sequence diversification of AvrLm3 and AvrLm4-7 under such a selection pressure, and identified a few regions of the AvrLm4-7 protein involved in both its recognition by Rlm7 and in its AvrLm3-Rlm3 masking ability. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Crossover rate between homologous chromosomes and interference are regulated by the addition of specific unpaired chromosomes in Brassica.

Recombination is a major mechanism generating genetic diversity, but the control of the crossover rate remains a key question. In Brassica napus (AACC, 2n = 38), we can increase the homologous recombination between A genomes in AAC hybrids. Hypotheses for this effect include the number of C univalent chromosomes, the ratio between univalents and bivalents and, finally, which of the chromosomes are univalents. To test these hypotheses, we produced AA hybrids with zero, one, three, six or nine additional C chromosomes and four different hybrids carrying 2n = 32 and 2n = 35 chromosomes. The genetic map lengths for each hybrid were established to compare their recombination rates. The rates were 1.4 and 2.7 times higher in the hybrids having C6 or C9 alone than in the control (0C). This enhancement reached 3.1 and 4.1 times in hybrids carrying six and nine C chromosomes, and it was also higher for each pair of hybrids carrying 2n = 32 or 2n = 35 chromosomes, with a dependence on which chromosomes remained as univalents. We have shown, for the first time, that the presence of one chromosome, C9 , affects significantly the recombination rate and reduces crossover interference. This result will have fundamental implications on the regulation of crossover frequency.

The dispensable chromosome of Leptosphaeria maculans shelters an effector gene conferring avirulence towards Brassica rapa.

Phytopathogenic fungi frequently contain dispensable chromosomes, some of which contribute to host range or pathogenicity. In Leptosphaeria maculans, the stem canker agent of oilseed rape (Brassica napus), the minichromosome was previously suggested to be dispensable, without evidence for any role in pathogenicity. Using genetic and genomic approaches, we investigated the inheritance and molecular determinant of an L. maculans-Brassica rapa incompatible interaction. Single gene control of the resistance was found, while all markers located on the L. maculans minichromosome, absent in the virulent parental isolate, co-segregated with the avirulent phenotype. Only one candidate avirulence gene was identified on the minichromosome, validated by complementation experiments and termed AvrLm11. The minichromosome was frequently lost following meiosis, but the frequency of isolates lacking it remained stable in field populations sampled at a 10-yr time interval, despite a yearly sexual stage in the L. maculans life cycle. This work led to the cloning of a new 'lost in the middle of nowhere' avirulence gene of L. maculans, interacting with a B. rapa resistance gene termed Rlm11 and introgressed into B. napus. It demonstrated the dispensability of the L. maculans minichromosome and suggested that its loss generates a fitness deficit.

Using probe genotypes to dissect QTL × environment interactions for grain yield components in winter wheat.

Yield is known to be a complex trait, the expression of which interacts strongly with environmental conditions. Understanding the genetic basis of these genotype × environment interactions, particularly under limited input levels, is a key objective when selecting wheat genotypes adapted to specific environments. Our principal objectives were thus: (1) to identify genomic regions [quantitative trait loci (QTL)] involving QTL × environment interactions (QEI) and (2) to develop a strategy to understand the specificity of these regions to certain environments. The two main components of yield were studied: kernel number (KN) and thousand-kernel weight (TKW). The Arche × Récital doubled-haploid population of 222 lines was grown in replicated field trials during 2000 and 2001 at three locations in France, under two nitrogen levels. The 12 environments were characterized in terms of water deficit, radiation, temperature and nitrogen stress based on measurements conducted on the four-probe genotypes: Arche, Récital, Ritmo and Soissons. A four-step strategy was developed to explain QTL specificity to some environments: (1) the detection of QTL for KN and TKW in each environment; (2) the estimation of genotypic sensitivities as the factorial regression slope of KN and TKW to environmental covariates and the detection of QTL for these genotypic sensitivities; (3) study of the co-locations of QTL for KN and TKW and of the QTL for sensitivities; in the event of a co-location partitioning the QEI, appropriate covariates were employed; (4) a description of the environments where QTL were detected for KN and TKW using the environmental covariates. A total of 131 QTL were found to be associated with KN, TKW and their sensitivity to environmental covariates across the 12 environments. Four of these QTL, for both KN and TKW, were located on linkage groups 1B, 2D1, 4B and 5A1, and displayed pleiotropic effects. Factorial regression explained from 15.1 to 83.2% of the QEI for KN and involved three major environmental covariates: cumulative radiation-days ±3 days at meiosis, cumulative degree-days >25°C ±3 days at meiosis and nitrogen stress at flowering. For TKW, 13.5-81.8% of the effect of the QEI was partitioned and involved three major environmental covariates: water deficit from flowering to the milk stage, cumulative degree-days >0°C from the milk stage to maturity and soil water deficit at maturity. A comparative analysis was then performed on the QTL detected during this and previous studies published on QEI and some interacting QTL may be common to different genetic backgrounds. Focusing on these QTL common to different genetic backgrounds would give some guidance to understand genotype × environment interaction.

Crossovers get a boost in Brassica allotriploid and allotetraploid hybrids.

Meiotic crossovers are necessary to generate balanced gametes and to increase genetic diversity. Even if crossover number is usually constrained, recent results suggest that manipulating karyotype composition could be a new way to increase crossover frequency in plants. In this study, we explored this hypothesis by analyzing the extent of crossover variation in a set of related diploid AA, allotriploid AAC, and allotetraploid AACC Brassica hybrids. We first used cytogenetic methods to describe the meiotic behavior of the different hybrids. We then combined a cytogenetic estimation of class I crossovers in the entire genome by immunolocalization of a key protein, MutL Homolog1, which forms distinct foci on meiotic chromosomes, with genetic analyses to specifically compare crossover rates between one pair of chromosomes in the different hybrids. Our results showed that the number of crossovers in the allotriploid AAC hybrid was higher than in the diploid AA hybrid. Accordingly, the allotetraploid AACC hybrid showed an intermediate behavior. We demonstrated that this increase was related to hybrid karyotype composition (diploid versus allotriploid versus allotetraploid) and that interference was maintained in the AAC hybrids. These results could provide another efficient way to manipulate recombination in traditional breeding and genetic studies.

Genetic regulation of meiotic cross-overs between related genomes in Brassica napus haploids and hybrids.

Although the genetic regulation of recombination in allopolyploid species plays a pivotal role in evolution and plant breeding, it has received little recent attention, except in wheat (Triticum aestivum). PrBn is the main locus that determines the number of nonhomologous associations during meiosis of microspore cultured Brassica napus haploids (AC; 19 chromosomes). In this study, we examined the role played by PrBn in recombination. We generated two haploid x euploid populations using two B. napus haploids with differing PrBn (and interacting genes) activity. We analyzed molecular marker transmission in these two populations to compare genetic changes, which have arisen during meiosis. We found that cross-over number in these two genotypes was significantly different but that cross-overs between nonhomologous chromosomes showed roughly the same distribution pattern. We then examined genetic recombination along a pair of A chromosomes during meiosis of B. rapa x B. napus AAC and AACC hybrids that were produced with the same two B. napus genotypes. We observed significant genotypic variation in cross-over rates between the two AAC hybrids but no difference between the two AACC hybrids. Overall, our results show that PrBn changes the rate of recombination between nonhomologous chromosomes during meiosis of B. napus haploids and also affects homologous recombination with an effect that depends on plant karyotype.