Identification and mapping of new genes for resistance to downy mildew in lettuce

Abstract

Key message Eleven new major resistance genes for lettuce downy mildew were introgressed from wild Lactuca species and mapped to small regions in the lettuce genome. Abstract Downy mildew, caused by the oomycete pathogen Bremia lactucae Regel, is the most important disease of lettuce (Lactuca sativa L.). The most effective method to control this disease is by using resistant cultivars expressing dominant resistance genes (Dm genes). In order to counter changes in pathogen virulence, multiple resistance genes have been introgressed from wild species by repeated backcrosses to cultivated lettuce, resulting in numerous near-isogenic lines (NILs) only differing for small chromosome regions that are associated with resistance. Low-pass, whole genome sequencing of 11 NILs was used to identify the chromosome segments introgressed from the wild donor species. This located the candidate chromosomal positions for resistance genes as well as additional segments. F2 segregating populations derived from these NILs were used to genetically map the resistance genes to one or two loci in the lettuce reference genome. Precise knowledge of the location of new Dm genes provides the foundation for marker-assisted selection to breed cultivars with multiple genes for resistance to downy mildew.

Identification of genetic loci in lettuce mediating quantitative resistance to fungal pathogens

“…Due to the lack of complete resistance phenotypes against broad host range necrotrophic fungal pathogens and very limited number of NLR genes shown to impact resistance, it was thought that NLR proteins and ETI are not important in defence against these pathogens (Mengiste 2012). However, in our data expression of multiple lettuce NLRs was shown to be correlated with resistance suggesting that, in addition to their well-known role in lettuce resistance against biotrophic pathogens (Simko et al 2013;Parra et al 2016Parra et al , 2021, NLR genes in lettuce may play a role in quantitative resistance against B. cinerea and S. sclerotiorum. NLRs show huge diversity both within a single genome and in populations, and a multitude of incomplete NLRs (lacking one or more of the canonical domains but thought to still be able to function as adapters or helpers for other NLRs) are also found in all plants (Baggs et al 2017).…”

“…In lettuce, QTL mapping has been used extensively to characterise dominant resistance phenotypes against the oomycete pathogen Bremia lactucae, which causes downy mildew. More than 30 downy mildew resistance genes have been identified (Parra et al 2016(Parra et al , 2021. However, mapping of genetic determinants of QDR in lettuce against B. cinerea or S. sclerotiorum is in its infancy.…”

Assuring the Food Safety of Crops Developed through Breeding

“…Yield is driven by a variety of intrinsic factors and response to pests and weather conditions. Breeding programs often focus on enhanced disease resistance; for example, downy mildew is the most important disease in lettuce, and lettuce production over the past 50 years has relied heavily on incorporating genes from wild species to improve resistance . Another example of the criticality of disease resistance for food security is the threat posed by Fusarium Head Blight to wheat; in 2020, USDA’s Agricultural Research Service announced identification of a gene that can be used to develop more blight resistant varieties of wheat .…”

Sequence of the Mitochondrial Genome of Lactuca virosa Suggests an Unexpected Role in Lactuca sativa’s Evolution

“…The presence of mitochondrial sequences inserted in the nuclear genome, also known as NUMTs (Nuclear MiTochondrial sequences), further complicates their assembly from total genomic data. This is a relatively lesser issue in Arabidopsis thaliana and its small nuclear genome of ±157 Mb (The Arabidopsis Genome Initiative, 2000; Bennett et al, 2003), but it is a different situation for plants with much bigger nuclear genomes, such as lettuce (2.9 Gb) (Reyes- Chin-Wo et al, 2017). There are two ways to work around this problem: choose a higher-throughput sequencing strategy to increase sequencing deep, or enrich the mtDNA concentration by extracting it from purified mitochondria.…”

“…It is established that L. serriola is one of the direct ancestors and the closest related species ( de Vries, 1990 ; Kesseli et al, 1991 ; de Vries and van Raamsdonk, 1994 ) and that hybrids L. sativa × L. serriola are self-fertile ( Thompson et al, 1941 ; Thompson, 1943 ). L. virosa and L. saligna are playing an important role in the development of lettuce cultivars, and especially in the introgression of resistance genes like the ones for Bremia lactucae ( Parra et al, 2021 ). However, a study based on RFLP markers suggested that L. sativa could have a polyphyletic origin, but without being able to identify other contributing species ( Kesseli et al, 1991 ).…”