Genetics of Resistance to Leaf Rust in Wheat: An Overview in a Genome-Wide Level

: Due to the global warming and dynamic changes in pathogenic virulence, leaf rust caused by Puccinia triticina has greatly expanded its epidermic region and become a severe threat to global wheat production. Genetic bases of wheat resistance to leaf rust mainly rely on the leaf rust resistance ( Lr ) gene or quantitative trait locus ( QLr ). Although these genetic loci have been insensitively studied during the last two decades, an updated overview of Lr/QLr in a genome-wide level is urgently needed. This review summarized recent progresses of genetic studies of wheat resistance to leaf rust. Wheat germplasms with great potentials for genetic improvement in resistance to leaf rust were highlighted. Key information about the genetic loci carrying Lr/QLr was summarized. A genome-wide chromosome distribution map for all of the Lr/QLr was generated based on the released wheat reference genome. In conclusion, this review has provided valuable sources for both wheat breeders and researchers to understand the genetics of resistance to leaf rust in wheat.


Introduction
Leaf rust, caused by biotrophic fungal pathogen Puccinia triticina Erikss., is one of the most wide-spread and severe diseases in wheat all over the world [1].The yield loss caused by leaf rust ranges from 5% to 20%, and reaches about 50% during epidemics [2].Compared with other rust diseases such as stripe rust and stem rust, leaf rust adapts to a more moderate temperature (10-25 • C).However, due to the global warming, leaf rust has greatly expanded its epidermic region and advanced its occurrence period [3].Generally, seedling plants of wheat are more vulnerable to rust diseases, and all of these changes have made leaf rust become a new threat to global wheat productions.
Rational application of genetic loci controlling wheat resistance to leaf rust in breeding practice is still the best choice for the disease control.In this review, pathogenic profile of P. triticina will be briefly introduced to demonstrate the life cycle of this fungal pathogen on wheat and alternative hosts.Types of wheat resistance to leaf rust will be classified based on plant stage, disease symptom, and the cloned resistance gene.Recent progress with regards to genetic studies of wheat resistance to leaf rust will be summarized on a genome-wide level.Resistant germplasms and genetic loci conferring leaf rust resistance will be highlighted.

Pathogenic Profile
Leaf rust has a complicated life cycle including asexual stage on wheat and sexual stage on alternative hosts (Figure 1a,b) [1].At the asexual stage, leaf rust infects wheat plant via its urediospores (Figure 1a).Urediospores can spread over long distances with air flow and re-infect wheat plants multiple times.Since leaf rust has a broad host range including wheat, barley, and their wild relatives, it can easily over-summer on grasses and volunteer crops.On the other hand, it normally over-winter on wheat as latent hypha or urediospores.At the sexual stage, leaf rust produces telia on wheat leaves in the late growing season (Figure 1a); teliospores from telia further infects alternative hosts including Thalictrum spp. or Leptopyrum fumarioides; pycnia/pycniospores and aecium/aeciospores can be formed on the alternative hosts; fertilization occur between pycniospores and receptive hyphae with opposite mating type combinations; aeciospores infect back to the host plants of wheat and produce uredium/urediospores to complete the life cycle (Figure 1b).

Pathogenic Profile
Leaf rust has a complicated life cycle including asexual stage on wheat and sexual stage on alternative hosts (Figure 1a,b) [1].At the asexual stage, leaf rust infects wheat plant via its urediospores (Figure 1a).Urediospores can spread over long distances with air flow and re-infect wheat plants multiple times.Since leaf rust has a broad host range including wheat, barley, and their wild relatives, it can easily over-summer on grasses and volunteer crops.On the other hand, it normally over-winter on wheat as latent hypha or urediospores.At the sexual stage, leaf rust produces telia on wheat leaves in the late growing season (Figure 1a); teliospores from telia further infects alternative hosts including Thalictrum spp. or Leptopyrum fumarioides; pycnia/pycniospores and aecium/aeciospores can be formed on the alternative hosts; fertilization occur between pycniospores and receptive hyphae with opposite mating type combinations; aeciospores infect back to the host plants of wheat and produce uredium/urediospores to complete the life cycle (Figure 1b).

Types of Wheat Resistance to Leaf Rust
Based on the physiological features, genetic determinations, and molecular mechanisms, wheat resistance to leaf rust can be classified into two types (Table 1): race-specific resistance and slow rusting resistance.The race-specific resistance follows the gene-forgene theory.Currently, most of the cloned Lr genes controlling this type of resistance, including Lr1, Lr10, Lr13, Lr21, Lr22a, and Lr42, encode nucleotide binding site leucinerich repeat (NBS-LRR) proteins [4][5][6][7][8][9].As modeled in Arabidopsis, upon directly or indirectly recognition of avirulence (Avr) proteins secreted by phytopathogens, NBS-LRR proteins form a homo-pentamer called resistosome, which penetrates the cell membrane of the responsive cells and eventually results in the observed hypersensitive responses (HR) or necrosis on wheat leaves [10].A recent protein crystallization study on wheat stem rust resistance protein Sr35 and its corresponding avirulent protein AvrSr35 revealed a similar resistosome structure [11].Besides these NBS-LRR proteins, another race-specific resistance gene, Lr14a, encodes a membrane-localized protein containing multiple ankyrin repeats and Ca 2+ channels [12].The other recently cloned high-resistant gene Lr9/Lr58 encodes a tandem kinase fusion protein [13].Notably, certain race-specific resistance genes are functioning only at seedling stage but lost their resistance against multiple Pt

Types of Wheat Resistance to Leaf Rust
Based on the physiological features, genetic determinations, and molecular mechanisms, wheat resistance to leaf rust can be classified into two types (Table 1): race-specific resistance and slow rusting resistance.The race-specific resistance follows the gene-forgene theory.Currently, most of the cloned Lr genes controlling this type of resistance, including Lr1, Lr10, Lr13, Lr21, Lr22a, and Lr42, encode nucleotide binding site leucine-rich repeat (NBS-LRR) proteins [4][5][6][7][8][9].As modeled in Arabidopsis, upon directly or indirectly recognition of avirulence (Avr) proteins secreted by phytopathogens, NBS-LRR proteins form a homo-pentamer called resistosome, which penetrates the cell membrane of the responsive cells and eventually results in the observed hypersensitive responses (HR) or necrosis on wheat leaves [10].A recent protein crystallization study on wheat stem rust resistance protein Sr35 and its corresponding avirulent protein AvrSr35 revealed a similar resistosome structure [11].Besides these NBS-LRR proteins, another race-specific resistance gene, Lr14a, encodes a membrane-localized protein containing multiple ankyrin repeats and Ca 2+ channels [12].The other recently cloned high-resistant gene Lr9/Lr58 encodes a tandem kinase fusion protein [13].Notably, certain race-specific resistance genes are functioning only at seedling stage but lost their resistance against multiple Pt pathotypes in the field at the adult plant stage.Others may keep their high resistance to leaf rust at the adult plant stage as hypersensitive adult plant resistance (APR) or all-stage (AS) race-specific resistance.Slow rusting resistance, also considered as APR in most cases, provides a lower level but more durable resistance in a non-race-specific manner only at the adult plant stage.Compare with the mentioned hypersensitive APR, rust infection and sporulation can be accomplished in a much delayed and reduced manner.It is normally controlled by quantitative trait loci (QTL) and provides broad-spectrum resistance to multiple pathogens.For instance, the first cloned leaf rust APR gene Lr34 encoding an ATP-binding cassette (ABC) transporter controls resistance to stripe rust, stem rust, powdery mildew, and spot blotch [14].The other cloned leaf rust APR gene Lr67 encodes a hexose transporter that forms hetero dimer with other functional transporters to reduce the uptake of glucose [15].
With advances in techniques of genomic sequencing and molecular biology, cloning of Lr genes or leaf rust resistance QTL (QLr) has become a more feasible task.It can be accomplished following multiple strategies such as classical map-based positional cloning, or rapid gene-cloning approaches including MutChromSeq, MutRenSeq, AgRenSeq and MutIsoSeq, or even whole genome sequencing [16].In this review, we have mainly focused on the research progresses of genetic determinations of wheat resistance to leaf rust during the last two decades.Genetic loci carrying Lr/QLr are summarized and introduced following a sub-genome and chromosome order to provide an overview on a genome-wide level.A tall Indian bread wheat cultivar 'Sujata' displayed high resistance to leaf rust at adult plant stage in the field.Two novel significant resistance loci on chromosomes 1AS (QLr.cim-1AS) and 7BL (QLr.cim-7BL), in combination with Lr46 and Lr67, were identified using simple sequence repeat (SSR) markers [17].A major QTL, QLr.cau-1AS, for slow rusting in wheat cultivar 'Luke' was mapped to chromosome 1AS using SSR markers [18].A genome-wide association study (GWAS) on a panel of 483 spring wheat genotypes revealed major QTLs for APR against leaf rust on chromosome 1A (QLr.ramp-1A.2),1B (QLr.ramp-1B.3),and 6A (QLr.ramp-6A.1)[19].Seedling/all-stage leaf rust resistance (AS) gene Lr10 was also located on the chromosome 1AS [5].Lr10 was successfully cloned and encoded a typical NBS-LRR protein.Interestingly, two different CC-NBS-LRR proteins were discovered to be essential for the Lr10-mediated resistance [20].

Lr/QLr on Chromosome 2A
Great number of genetic loci carrying Lr/QLr was enriched on chromosome 2A.Lr65 originated from spelt wheat (Triticum spelta) was recently fine mapped within a 0.8 cM interval on chromosome 2AS, corresponding to a 60.11 Kb region in the Chinese Spring (CS) wheat reference genome [26].Lr37 introgressed from Aegilops ventricosa was initially mapped on the chromosome 2AS using restriction fragment length polymorphism (RFLP) and cleaved amplified polymorphic sequence (CAPS) markers [27].The chromosome 2AS-located Lr17a gene was widely presented in wheat varieties adapted to North America and its resistance has been overcome by newly merged Pt pathotypes [28].Seedling resistance gene Lr81 was identified from a Croatian breeding line 'PI 470121 and mapped to an approximately 100 Kb genomic region on chromosome 2AS using Kompetitive allele-specific PCR (KASP) markers [29].A novel leaf rust resistance gene LrM introgressed from Ae. markgrafii provides high degree of resistance against multiple Pt pathotypes.LrM was mapped on chromosome 2AS using SSR-and SNP-based PCR markers [30].Seedling resistance gene Lr45 was derived from Secale cereale and introgressed into chromosome 2AS [31].

Lr/QLr on Chromosome 4A
A novel seedling resistance gene Lr.ace-4A for multiple Pt isolates was initially detected on chromosome 4A from a Portuguese durum landrace 'PI 192051' [41].A diversity panel of 268 wheat lines was evaluated for leaf rust resistance at both seedling and adult plant stages.A GWAS using 90K SNP array revealed novel QTLs for APR on chromosomes 4AL (QLr.zha-4AL) and 1DL (QLr.zha-1DL)[42].Seedling resistance gene Lr28 derived from Ae. speltoides was mapped to chromosome 4AL, and a microsatellite marker was validated to be closely linked to this gene [43].Moreover, the possible molecular mechanism of Lr28 has been intensively investigated during the last decade with emphasis on its transcriptional responses [44,45].

Lr/QLr on Chromosome 6A
Seedling resistance gene Lr62 was transferred from Ae. neglecta and mapped to chromosome 6AS using microsatellite markers [51].The Ae. sharonensis-derived seedling resistance gene Lr56 was translocated to the telomeric region of chromosome 6AL [52].Another AS gene Lr64 initially introgressed from T. dicoccoides was also mapped to chromosome 6AL with SNP and KASP markers [53].

Lr/QLr on Chromosome 7A
Seedling resistance gene Lr47 was introgressed from Ae. speltoides to chromosome 7AS [54].Grain yields and flour quality were negatively influenced by the introgression of chromosome segment carrying Lr47 [55].Nevertheless, this gene still showed high resistance to most of the collected Pt pathotypes in China and its transcriptional regulatory network was profiled [56].A recent study developed new KASP markers for the Lr47 gene [57].A large scale association studies using 1032 spring wheat accessions and 9K SNP array revealed QTLs on chromosome 7AS (QLr.tur-7AS) and 2DL (QLr.tur-2DL)contributed to both seedling resistance and APR to leaf rust [58].Seedling resistance gene Lr20 was localized in the distal region of chromosome 7AL [59].Recombination of the genetic locus carrying Lr20 was significantly suppressed, indicating this chromosome segment may be introgressed from unidentified wild relative species.
Information about all of the genetic loci carrying Lr and major QLr in A sub-genome was summarized in Table 2. Chromosome distributions of these genetic loci in A subgenome were estimated based on the positions of associated molecular markers in the common wheat Chinese Spring reference genome v1.1 (Figure 2).
a Bold labeled molecular markers were used for generating the distribution map of Lr/QLr.S1).Numbers on the left side of each chromosome indicated physical locations in units of 10,000,000 bp.Formally designated Lr genes are highlighted in red, and stable QTLs with large effect are in green.

Lr/QLr on Chromosome 1B
Genetic loci carrying Lr/QLr were intensively distributed on chromosome 1B.Seedling resistance gene Lr55 derived from Elymus trachycaulus was mapped to chromosome 1BS using microsatellite and DArT-based markers [60].A recent study revealed that Lr33 on chromosome 1BL conferred resistance to leaf rust at both seedling and adult plant stages [61].Interestingly, Lr44 originated from spelt wheat 'Accession 7831′ was reported as recessive or partially dominant to Lr33 [62].Seedling resistance gene Lr71 was identified from spelt wheat cultivar 'Altgold Rotkorn'.It was initially mapped close to the centromere of chromosome 1B using SSR markers and deletion lines [63].A major QTL  S1).Numbers on the left side of each chromosome indicated physical locations in units of 10,000,000 bp.Formally designated Lr genes are highlighted in red, and stable QTLs with large effect are in green.Genetic loci carrying Lr/QLr were intensively distributed on chromosome 1B.Seedling resistance gene Lr55 derived from Elymus trachycaulus was mapped to chromosome 1BS using microsatellite and DArT-based markers [60].A recent study revealed that Lr33 on chromosome 1BL conferred resistance to leaf rust at both seedling and adult plant stages [61].Interestingly, Lr44 originated from spelt wheat 'Accession 7831 was reported as recessive or partially dominant to Lr33 [62].Seedling resistance gene Lr71 was identified from spelt wheat cultivar 'Altgold Rotkorn'.It was initially mapped close to the centromere of chromosome 1B using SSR markers and deletion lines [63].A major QTL QLr.sfr-1BS was discovered in winter wheat cultivar 'Forno' for APR to leaf rust in a series of genetic studies and eventually designated as Lr75 [64,65].Interestingly, a consistently detected QTL QLr.pser-1BL controlling phenotype of lesion mimics in wheat cultivar 'Ning7840 was also responsible for seedling resistance and APR to leaf rust [66].A seedling resistance gene LrZH84 was identified from a widely planted wheat cultivar 'Zhou 8425B' in China and mapped to chromosome 1BL using multiple molecular markers [67,68].

Genetic Loci Carrying
Lr46 was another slow rusting gene that conferred broad-spectrum resistance to multiple fungal diseases, including stripe rust (Yr29), stem rust (Sr58), powdery mildew (Pm39), and spot blotch (Qsb).Various molecular markers have been developed to map this genetic locus or utilize it in breeding programs [69,70].Major QTLs for slow rusting detected in wheat cultivars 'Bainong 64 and 'Attila' were both initially mapped to chromosome 1BL and further predicted as Lr46 [71,72].Seedling resistance gene Lr51 introgressed from Ae. speltoides was mapped to chromosome 1BL and its associated CAPS marker was designed [73].Seedling resistance gene Lr26 was derived from rye (S. cereale) and located on the 1BL/1RS translocation in wheat [74].The recent released high-quality genome assembly of rye may greatly facilitate the cloning of Lr26 in the coming future [75].A multiple-year stable major QTL QLr.pbi-1B for APR of wheat cultivar 'Beaver' was mapped to chromosome 1BL and estimated to be associated with the 1BL/1RS translocation [46].

Lr/QLr on Chromosome 2B
Chromosome 2BS is a hot zone enriched with large number of Lr/QLr loci.Three wheat cultivars from different regions, including 'Saragolla' from Italy, 'Gaza' from the Middle East, and 'Arnacoris' from France, expressed high levels of resistance to Mexican races of P. triticina.Further genetic investigation revealed major APR QTLs on chromosomes 2BS (QLr.usw-2BS),6BS (QLr.usw-6BS),6BL (QLr.usw-6BL), and 7BL (QLr.usw-7BL)[76].Lr16 was a seedling resistance gene previously mapped to the telomeric region of chromosome 2BS [77].A recent genetic study using four mapping populations developed resistance gene analog (RGA)-based SNP markers associated with Lr16 to facilitate the marker-assisted selection (MAS) [78].A major QTL QLr.csiro-2BS on chromosome 2BS for slow rusting was discovered in wheat cultivar 'Attila' [72].Lr48 was designated as a hypersensitive APR gene and mapped to chromosome 2BS using SSR markers [79].An International Maize and Wheat Improvement Center (CIMMYT) spring wheat line 'Shanghai 3/Catbird' showed a high level of APR to Chinese P. triticina pathotypes in the field.A major QTL QLr.hebau-2BS was detected on chromosome 2BS using SSR markers [80].Seedling resistance gene Lr23 on chromosome 2BS was initially identified from a synthetic hexaploid wheat 'W-7984 produced from the cross between durum wheat cultivar 'Altar 84 and Ae.tauschii [81].A further investigation discovered a major QTL QLr.ksu-2BS for APR in 'W-7984 close to Lr23 [82].
The chromosome 2BS-located Lr13 was sufficient to provide seedling resistance at relatively high temperature around 25 • C and APR in the field.This gene encoding a typical NBS-LRR protein also controlled hybrid necrosis as a specific allele of Necrosis 2 (Ne2) [6,83].An Argentinean wheat cultivar 'Klein Proteo' showed broad-spectrum resistance to most of the Chinese P. triticina pathotypes at seedling stage.A single-dominant gene LrKP was mapped near the Lr13 region on chromosome 2BS.Its relationship to Lr13 remained to be explored [84].The APR gene Lr35 was introgressed from Ae. speltoides and showed broad resistance to different Pt pathotypes.The Lr35 gene was mapped to chromosome 2BS using RFLP and STS markers [85].Several pathogenesis-related protein (PR) genes including PR1, PR2, and PR5 were reported to be involved in the Lr35-mediated APR response [86][87][88].A chromosome 2BS-located major QTL QLr.osu-2B for slow rusting was consistently detected from wheat line 'CI 13227 in multiple environments [89].
A diverse panel of 196 spring wheat genotypes was phenotyped for the leaf rust resistance in the field.A GWAS using 90K SNP array revealed significant associations with multiple SNPs on chromosomes 2B (QLr.dms-2B.2) and 2D (QLr.dms-2D)[90].An AS gene LrNJ97 was identified from a Chines wheat line 'Neijiang 977671 and linked with SSR markers on chromosome 2BL [91].Seedling resistance gene Lr50 was introgressed from T. timopheevii subsp.armeniacum and initially mapped on chromosome 2BL using SSR markers [92].

Lr/QLr on Chromosome 4B
A major QTL QLr.sfrs-4B for APR in wheat cultivar 'Forno' was detected on chromosome 4B [39].Lr12 on chromosome 4BL provides adult-plant race-specific resistance to leaf rust.It is completely linked or identical to Lr31, whose seedling resistance is associated with another complementary gene Lr27 [99].A recent study detected a major QTL QLr.hebau-4B on chromosome 4BL for APR in wheat cultivar 'Chinese Spring' and its relationship to Lr12 remained to be tested [34].The seedling resistance gene Lr25 was originally transferred from Secale cereale and linked with SSR markers on chromosome 4BL [100].The APR gene Lr49 was discovered in wheat recombinant inbred line 'VL404 and also mapped to chromosome 4BL using SSR markers [79].
The Ae. umbellulata-derived gene Lr9 was introgressed to chromosome 6BL and recently cloned using mutagenesis and transcriptome sequencing.It encoded an unusual tandem kinase fusion protein, and the coding sequence was identical to gene Lr58 introgressed from Ae. triuncialis on chromosome 2BL [13,108].Two consistent major QTLs for APR were detected in wheat cultivar 'Pastor' on chromosomes 6BL (QLr.cimmyt-6BL.1)and 7BL (QLr.cimmyt-7BL)[109].The chromosome 6BL-located Lr3 had three alleles as Lr3a, Lr3bg, and Lr3ka.Since this gene has not been cloned yet, it was difficult to distinguish different alleles [110].

Lr/QLr on Chromosome 7B
The seedling resistance gene Lr72 was discovered in durum wheat cultivar 'Atil C2000 and mapped to chromosome 7BS using SSR markers [111].A consistently detected QTL QLr.sfrs-7B.2was discovered to confer APR in wheat cultivar 'Forno' [39].A major QTL QLr.cimmyt-7BL.1 for slow rusting in wheat cultivar 'Parula' was detected on chromosome 7BL as a possible homoallele to Lr34 [112].Wheat line 'CI 13227 showed a high leveled slow rusting resistance.A stable QTL QLr.osu-7BL/QLrlp.osu-7BLon the chromosome 7BL was consistently detected in a series of studies [89,113].The chromosome 7BL-located AS gene Lr14a has been cloned recently using the sequenced genome of wheat line 'ArinaLrFor'.It encoded a membrane-localized protein containing twelve ankyrin repeats and Ca 2+permeable non-selective cation channels-like structures.Its unique mechanism controlling race-specific disease resistance remained to be explored [12].The slow rusting gene Lr68 was isolated from wheat cultivar 'Parula' and mapped to the distal region of chromosome 7BL [114].QLr.ubo-7B.2 was a major QTL on chromosome 7BL responsible for both seedling resistance and APR in durum wheat cultivar 'Colosseo' [115].A postulated novel seedling resistance gene LrFun from wheat cultivar 'Fundulea 900 was also mapped to the distal region of chromosome 7BL [116].A cluster of defense response genes including catalase, chitinase, thaumatin, and ion channel regulator on chromosome 7BL was associated with APR of wheat cultivar 'Opata 85 to leaf rust as a major QTL QLr.ksu-7BL [82].
Information about all of the genetic loci carrying Lr and major QLr in B sub-genome was summarized in Table 3. Chromosome distributions of these genetic loci in B subgenome were estimated based on the positions of associated molecular markers in the common wheat Chinese Spring reference genome v1.1 (Figure 3).
a Bold labeled molecular markers were used for generating the distribution map of Lr/QLr.S1).Numbers on the left side of each chromosome indicated physical locations in units of 10,000,000 bp.Formally designated Lr genes are highlighted in red, and stable QTLs with large effect are in green.

Genetic Loci Carrying
Lr/QLr in D Sub-Genome

Lr/QLr on Chromosome 1D
There were several seedling resistance Lr genes in the distal region of chromosome 1DS.Both Lr21 and Lr40 were introgressed from Ae. tauschii, and later they were proved to be allelic to each other [118].Lr21 was then successfully cloned and encoded a typical NBS-LRR protein [7].By developing a virus-induced gene-silencing (VIGS) system, a protein complex of RAR1-SGT1-HSP90 was proved to be essential for the full function of Lr21 [119].Lr60, also known as LrW2, was mapped to a nearby region of Lr21 on chromosome 1DS using microsatellite markers [120].Seedling resistance gene LrTs276-2 was derived from T. spelta and initially mapped to chromosome 1DS using BSA [121].Another Ae. tauschiiderived seedling resistance gene Lr42 located in this region was recently cloned using BSR-seq on constructed Ae. taushchii mapping populations [9].The Lr42 gene also encoded a typical NBS-LRR protein and was widely employed in wheat breading practice.S1).Numbers on the left side of each chromosome indicated physical locations in units of 10,000,000 bp.Formally designated Lr genes are highlighted in red, and stable QTLs with large effect are in green.

Genetic Loci Carrying
Lr/QLr in D Sub-Genome 6.1.Lr/QLr on Chromosome 1D There were several seedling resistance Lr genes in the distal region of chromosome 1DS.Both Lr21 and Lr40 were introgressed from Ae. tauschii, and later they were proved to be allelic to each other [118].Lr21 was then successfully cloned and encoded a typical NBS-LRR protein [7].By developing a virus-induced gene-silencing (VIGS) system, a protein complex of RAR1-SGT1-HSP90 was proved to be essential for the full function of Lr21 [119].Lr60, also known as LrW2, was mapped to a nearby region of Lr21 on chromosome 1DS using microsatellite markers [120].Seedling resistance gene LrTs 276-2 was derived from T. spelta and initially mapped to chromosome 1DS using BSA [121].Another Ae. tauschii-derived seedling resistance gene Lr42 located in this region was recently cloned using BSR-seq on constructed Ae. taushchii mapping populations [9].The Lr42 gene also encoded a typical NBS-LRR protein and was widely employed in wheat breading practice.

Lr/QLr on Chromosome 2D
A large number of genetic loci carrying Lr/QLr was distributed on chromosome 2D, particularly in the distal region of the short arm.The AS gene Lr11 in common wheat cultivar 'Buck Poncho' was recently re-mapped to chromosome 2DS using BSR-seq and multiple molecular markers [122].Two major QTLs, QLrlp.osu-2DS and QLrid.osu-2DS, for slow rusting in the recombinant inbred line 'CI 13227 were mapped to the distal region of chromosome 2DS [89,113].The AS gene Lr80 showed widely effective resistance to multiple Pt pathotypes and was initially mapped to the chromosome 2DS using SSR and 90K SNP markers [123].Both seedling resistance genes Lr39 and Lr41 were transferred from Ae. tauschii and reported later as the same or closely linked genes on chromosome 2DS [124,125].Another study predicted that Lr39, although introgressed to a different chromosome, was an allelic gene to Lr21 [118].An APR locus QLr.cim-2DS contributed by an adapted common wheat line 'UC1110 was genetically mapped to chromosome 2DS using a segregation population [126].Lr2a located on chromosome 2DS was reported to be involved in both seedling resistance and APR (QLr.mna-2DS).A major QTL QLr.inra-2D on chromosome 2DS was responsible for the APR in wheat cultivar 'Balance' [127].The seedling resistance gene Lr22a derived from Ae. tauschii was successfully cloned using the 'targeted chromosomebased cloning via long-range assembly (TACCA)' approach [8].The Lr22a gene encoded an intercellular immune receptor with an NBS-LRR structure.Seedling resistance gene Lr15 was also mapped to chromosome 2DS using SSR markers [128].A major QTL QLr.hwwg-2DS responsible for slow rusting was detected in the U.S. winter wheat line 'CI13227 using 90K SNP and SSR markers [129].The AS gene Lr54 was introgressed from Aegilop kotschyi to chromosome 2DL.A dominant sequence characterized amplified region (SCAR) marker and three microsatellite markers were developed to detect Lr54 [130].

Lr/QLr on Chromosome 3D
AS gene Lr32 introgressed from Ae. tauschii was mapped to the short arm of chromosome 3D [131].A Chinese wheat cultivar 'Pingyuan 50 showed APR to multiple fungal diseases including stripe rust, powdery mildew, and leaf rust.A major QTL QLr.hebau-3DS was stably detected in six experimental environments using 55K SNP array and additional SSR markers [132].In wheat cultivar 'UC1110 , besides QLr.cim-2DS, there was a co-located APR locus QLr.cim-3DC/QYr.cim-3DCon centromere region of chromosome 3D to both leaf rust and stripe rust [126].Moreover, QLr.cim-3DC and QLr.cim-2DS showed marginally significant interaction for APR in 'UC1110 .AS gene Lr24 derived from Agropyron elongatum was mapped in the distal region of chromosome 3DL [133].A further study developed SCAR markers co-segregating with the Lr24 gene [134], and this gene was widely used in breeding practice.

Lr/QLr on Chromosome 4D
The Lr67 gene on chromosome 4DL provided slow rusting resistance to leaf rust and was successfully cloned recently [15].It encodes a hexose transporter to block the uptake of glucose by rust fungus.A major QTL QLr.sfrs-4DL for APR in wheat cultivar 'Forno' was constantly detected on chromosome 4DL in different environments [39].

Lr/QLr on Chromosome 5D
Several AS genes were mapped to chromosome 5D.Seedling resistance gene Lr70 was discovered in common wheat accession 'KU3198 and mapped to chromosome 5DS using BSA [135].An Ae. umbellulate-derived AS gene Lr76 was transferred to the telomeric region of chromosome 5DS [136].The Lr78 gene was identified as an APR gene controlling slow rusting in wheat cultivar 'Toropi'.It was also mapped to chromosome 5DS using SSR and KASP markers [137].The Lr57 gene derived from Aegilops geniculata conferred both seedling resistance and APR to leaf rust.It was introgressed to chromosome 5D and co-segregated RFLP markers were developed for this gene [138].The chromosome 5DL-located Lr1 has been successfully cloned using classical map-based positional cloning strategy [4].The seedling resistance Lr1 gene also encoded a typical NBS-LRR protein, and its function was validated using a VIGS assay.

Lr/QLr on Chromosome 6D
The Chinese wheat landrace 'Bai Qimai' showed a slow rusting phenotype at the adult plant stage, and a major QTL QLr.cau-6DL on chromosome 6DL was recently identified using 90K SNP chip and SSR markers [139].The A. intermedium-derived Lr38 on chromosome 6DL provided a stable seedling and APR to multiple Pt pathotypes [140].

Lr/QLr on Chromosome 7D
A multiparent advanced generation intercross (MAGIC) wheat population was generated comprising 394 F 6:8 RILs and a total of 19 QTLs were detected on 11 distinct chromosomal regions.Among these QTLs, a major QTL QLr.jki-7D.1 on chromosome 7D explained 28% of the phenotypic variance with 'BAYP4535 as the most resistant founder [141].There were three designated Lr genes on chromosome 7D.The slow rusting gene Lr34 located on chromosome 7DS was successfully cloned and widely used in wheat breeding all over the world [14].It encoded an ABC transporter and was associated with leaf tip necrosis.The phytohormone abscisic acid (ABA) was recently revealed as a substrate of the ABC transporter encoded by Lr34, and the re-distribution of ABA in the Lr34-expressing plant greatly influenced the transcriptional response [142].Moreover, Lr34 also showed excellent potentials for genetic improvement in disease resistance of several other crops, including maize to common rust and northern corn leaf blight [143], sorghum to anthracnose and rust [144], and rice to blast disease [145].
Both seedling resistance genes Lr29 and Lr19 were transferred from A. elongatum to chromosome 7D.Lr29 was mapped to chromosome 7DS using random amplified polymorphic DNA (RAPD) and SCAR markers [146].Lr19 located on chromosome 7DL still provided high resistance to major Pt pathotypes in worldwide, and various molecular markers were developed for this gene to facilitate its usage in breeding practice [147,148].Notably, the same A. elongatum-derived chromosome segment carrying Fusarium head blight resistance gene 7 (Fhb7) was successfully decoded recently, which might greatly facilitate the cloning of Lr19 in the future [149].
Information about all of the genetic loci carrying Lr/QLr in D sub-genome was summarized in Table 4. Chromosome distributions of these genetic loci in D sub-genome were estimated based on the positions of associated molecular markers in the common wheat Chinese Spring reference genome v1.1 (Figure 4).S1).Numbers on the left side of each chromosome indicated physical locations in units of 10,000,000 bp.Formally designated Lr genes are highlighted in red, and stable QTLs with large effect are in green.

Discussion
Future application of wheat leaf rust resistance genes requires more efficient co-operations between wheat researchers and breeders.In recent years, many Lr/QLr have been identified and linked molecular markers have been developed.Knowledge regarding the sources and distribution of leaf rust resistance genes are important for developing new wheat cultivars with resistance.Wild wheat relatives are still valuable sources of novel genetic loci carrying Lr/QLr.Resistant germplasms including introgression lines generated from wheat relatives remain to be explored.With recent progresses of sequenced genomes of wheat relatives/progenitors, more resistance genes are expected to be cloned from these sources [151].Previous issues such as long breeding periods and drawback from unwanted chromosome introgression will be solved by potential linkage drag with advanced techniques in speed breeding [152].S1).Numbers on the left side of each chromosome indicated physical locations in units of 10,000,000 bp.Formally designated Lr genes are highlighted in red, and stable QTLs with large effect are in green.

Discussion
Future application of wheat leaf rust resistance genes requires more efficient cooperations between wheat researchers and breeders.In recent years, many Lr/QLr have been identified and linked molecular markers have been developed.Knowledge regarding the sources and distribution of leaf rust resistance genes are important for developing new wheat cultivars with resistance.Wild wheat relatives are still valuable sources of novel genetic loci carrying Lr/QLr.Resistant germplasms including introgression lines generated from wheat relatives remain to be explored.With recent progresses of sequenced genomes of wheat relatives/progenitors, more resistance genes are expected to be cloned from these sources [151].Previous issues such as long breeding periods and drawback from unwanted chromosome introgression will be solved by potential linkage drag with advanced techniques in speed breeding [152].
As indicated on the genome-wide scale map in this study (Figures 2-4), we have overviewed Lr/QLr on a genome-wide level and found several hot zones enriched with Lr/QLr such as chromosomes 2AS, 2BS, 7BL, and 2DS.Pyramids of race-specific resistance and slow rusting resistance are expected to be an effective strategy for breeding durable resistance.Rational pyramiding of these leaf rust resistance loci with balanced seedling resistance and slow rusting resistance relies on further development of high-throughput SNP-based molecular markers.With advanced techniques in genome sequencing and molecular biology, more Lr genes or dominant genes in QLr loci are expected to be cloned in the coming future.Seedling resistance genes may even be modified based on their molecular interactions with corresponding Avr proteins from P. triticina.On the other hand, the general durability of all of the APR genes should not be complacent [153].Transgenic expression of clustered R gene cassette is another strategy to provide broad-spectrum resistance to multiple rust pathotypes [154].Gene-editing on susceptible genes or negative regulatory genes of plant defense responses shows great potentials in improvement of wheat resistance to fungal diseases [155].

Conclusions
In conclusion, this review summarized recent progresses of genetics of wheat resistance to leaf rust on a genome-wide perspective.It will serve as a valuable resource for both researchers and breeders to follow-up studies on various genetic loci controlling resistance of wheat to leaf rust.

Figure 1 .
Figure 1.Pathogenic profile of Puccinia triticina.(a) Leaf rust infects wheat leaves via its urediospores at the asexual stage.Telia is produced on wheat leaves in the late growing season.(b) Life cycle of P. triticina can be divided into asexual stage on wheat and sexual stage on alternative hosts.Teliospores infect alternative hosts Thalictrum spp.and later produces pycnia and aecium.Aeciospores infect back to wheat plants to complete the life cycle.

Figure 1 .
Figure 1.Pathogenic profile of Puccinia triticina.(a) Leaf rust infects wheat leaves via its urediospores at the asexual stage.Telia is produced on wheat leaves in the late growing season.(b) Life cycle of P. triticina can be divided into asexual stage on wheat and sexual stage on alternative hosts.Teliospores infect alternative hosts Thalictrum spp.and later produces pycnia and aecium.Aeciospores infect back to wheat plants to complete the life cycle.

Figure 2 .
Figure 2. Genome-wide distribution of genetic loci carrying Lr/QLr in A sub-genome of wheat (Chromosomes 1A-7A).Molecular markers, SNPs, and genes associated with Lr/QLr were collected from previous publications and searched against the reference genome of common wheat 'Chinese Spring' v1.1.Corresponding physical position of each Lr/QLr was estimated, and a distribution map was generated using MapChart software v2.32 (raw data in TableS1).Numbers on the left side of each chromosome indicated physical locations in units of 10,000,000 bp.Formally designated Lr genes are highlighted in red, and stable QTLs with large effect are in green.

Figure 2 .
Figure 2. Genome-wide distribution of genetic loci carrying Lr/QLr in A sub-genome of wheat (Chromosomes 1A-7A).Molecular markers, SNPs, and genes associated with Lr/QLr were collected from previous publications and searched against the reference genome of common wheat 'Chinese Spring' v1.1.Corresponding physical position of each Lr/QLr was estimated, and a distribution map was generated using MapChart software v2.32 (raw data in TableS1).Numbers on the left side of each chromosome indicated physical locations in units of 10,000,000 bp.Formally designated Lr genes are highlighted in red, and stable QTLs with large effect are in green.

Figure 3 .
Figure 3. Genome-wide distribution of genetic loci carrying Lr/QLr in B sub-genome of wheat (Chromosomes 1B-7B).Molecular markers, SNPs, and genes associated with Lr/QLr were collected from previous publications and searched against the reference genome of common wheat 'Chinese Spring' v1.1.Corresponding physical position of each Lr/QLr was estimated, and a distribution map was generated using MapChart software v2.32 (raw data in TableS1).Numbers on the left side of each chromosome indicated physical locations in units of 10,000,000 bp.Formally designated Lr genes are highlighted in red, and stable QTLs with large effect are in green.

Figure 3 .
Figure 3. Genome-wide distribution of genetic loci carrying Lr/QLr in B sub-genome of wheat (Chromosomes 1B-7B).Molecular markers, SNPs, and genes associated with Lr/QLr were collected from previous publications and searched against the reference genome of common wheat 'Chinese Spring' v1.1.Corresponding physical position of each Lr/QLr was estimated, and a distribution map was generated using MapChart software v2.32 (raw data in TableS1).Numbers on the left side of each chromosome indicated physical locations in units of 10,000,000 bp.Formally designated Lr genes are highlighted in red, and stable QTLs with large effect are in green.

Figure 4 .
Figure 4. Genome-wide distribution of genetic loci carrying Lr/QLr in D sub-genome of wheat (Chromosomes 1D-7D).Molecular markers, SNPs, and genes associated with Lr/QLr were collected from previous publications and searched against the reference genome of common wheat 'Chinese Spring' v1.1.Corresponding physical position of each Lr/QLr was estimated, and a distribution map was generated using MapChart software v2.32 (raw data in TableS1).Numbers on the left side of each chromosome indicated physical locations in units of 10,000,000 bp.Formally designated Lr genes are highlighted in red, and stable QTLs with large effect are in green.

Figure 4 .
Figure 4. Genome-wide distribution of genetic loci carrying Lr/QLr in D sub-genome of wheat (Chromosomes 1D-7D).Molecular markers, SNPs, and genes associated with Lr/QLr were collected from previous publications and searched against the reference genome of common wheat 'Chinese Spring' v1.1.Corresponding physical position of each Lr/QLr was estimated, and a distribution map was generated using MapChart software v2.32 (raw data in TableS1).Numbers on the left side of each chromosome indicated physical locations in units of 10,000,000 bp.Formally designated Lr genes are highlighted in red, and stable QTLs with large effect are in green.

Table 1 .
Types of wheat resistance to leaf rust.

Table 2 .
Genetic loci carrying Lr/QLr in A sub-genome.

Table 3 .
Genetic loci carrying Lr/QLr in B sub-genome.

Table 4 .
Genetic loci carrying Lr/QLr in D sub-genome.