Disease resistance loci in onion

Abstract

The present disclosure provides for unique onion plants with disease resistance and desirable bulb color and their progeny. Such plants may comprise an introgressed QTL associated with multiple disease resistance coupled with a desirable bulb color. In certain aspects, compositions, including distinct polymorphic molecular markers, and methods for producing, breeding, identifying, selecting, and the like of plants or germplasm with disease resistance and/or desirable bulb color are provided.

1 . An onion plant comprising resistance to  Fusarium  basal rot and pink root, wherein the plant further comprises lack of the complementary pinks trait. 
     
     
         2 . The onion plant of  claim 1 , wherein said onion plant:
 (a) comprises a cis-coupled linkage comprising resistance to  Fusarium  basal rot conferred by said onion genomic region defined by loci NQ0345038 (SEQ ID NO:3) and NQ0257326 (SEQ ID NO:23) on linkage group 2 (LG2), resistance to pink root conferred by said onion genomic region defined by loci NQ0257277 (SEQ ID NO:22) and NQ0258453 (SEQ ID NO:27) on linkage group 2 (LG2), and lack of the complimentary pinks bulb color conferred by said onion genomic region defined by loci NQ0257220 (SEQ ID NO:26) and NQ0257692 (SEQ ID NO:29) on linkage group 2 (LG2);   (b) is a hybrid or an inbred; or   (c) is an agronomically elite line.   
     
     
         3 . The onion plant of  claim 2 , wherein said cis-coupled linkage is introgressed into an onion variety selected from the group consisting of North American Yellow and Universal Yellow. 
     
     
         4 . A part of the onion plant of  claim 1 , further defined as pollen, an ovule, a leaf, an embryo, a root, a root tip, an anther, a flower, a bulb, a stem, a shoot, a seed, a protoplast, a cell, and a callus. 
     
     
         5 .- 6 . (canceled) 
     
     
         7 . An onion plant comprising in its genome at least one introgressed allele locus, wherein said introgressed allele locus comprises:
 an onion genomic region defined by loci NQ0345038 (SEQ ID NO:3) and NQ0257326 (SEQ ID NO:23) on linkage group 2 (LG2), conferring resistance to  Fusarium  basal rot (FBR);   an onion genomic region defined by loci NQ0257277 (SEQ ID NO:22) and NQ0258453 (SEQ ID NO:27) on linkage group 2 (LG2), conferring resistance to Pink Root (PR);   an onion genomic region defined by loci NQ0257220 (SEQ ID NO:26) and NQ0257692 (SEQ ID NO:29) on linkage group 2 (LG2) conferring lack of the Complimentary Pinks bulb color;   an onion genomic region defined by loci NQ0258523 (SEQ ID NO:30) and NQ0345206 (SEQ ID NO:36) on linkage group 3 (LG3), conferring resistance to  Fusarium  basal rot (FBR);   an onion genomic region defined by loci NQ0345564 (SEQ ID NO:38) and NQ0257917 (SEQ ID NO:63) on linkage group 4 (LG4), conferring resistance to  Fusarium  basal rot (FBR);   an onion genomic region defined by loci NQ0344978 (SEQ ID NO:49) and NQ0344766 (SEQ ID NO:55) on linkage group 4 (LG4), conferring resistance to Pink Root (PR);   an onion genomic region defined by loci NQ0258361 (SEQ ID NO:37) and NQ0344778 (SEQ ID NO:61) on linkage group 4 (LG4) conferring production or inhibition of bulb color;   or   an onion genomic region defined by loci NQ0257378 (SEQ ID NO:64) and NQ0345734 (SEQ ID NO:74) on linkage group 6 (LG6) conferring a red pigment bulb color;   or a progeny plant therefrom.   
     
     
         8 . The onion plant of  claim 7 , wherein said plant:
 (a) comprises a cis-coupled linkage comprising resistance to  Fusarium  basal rot (FBR) conferred by said onion genomic region defined by loci NQ0345038 (SEQ ID NO:3) and NQ0257326 (SEQ ID NO:23) on linkage group 2 (LG2), resistance to Pink Root conferred by said onion genomic region defined by loci NQ0257277 (SEQ ID NO:22) and NQ0258453 (SEQ ID NO:27) on linkage group 2 (LG2), and lack of the Complimentary Pinks bulb color conferred by said onion genomic region defined by loci NQ0257220 (SEQ ID NO:26) and NQ0257692 (SEQ ID NO:29) on linkage group 2 (LG2);   (b) is a hybrid or an inbred; or   (c) is an agronomically elite line.   
     
     
         9 . The onion plant of  claim 8 , wherein said cis-coupled linkage is introgressed into an onion variety selected from the group consisting of North American Yellow and Universal Yellow. 
     
     
         10 . A part of the onion plant of  claim 7 , further defined as pollen, an ovule, a leaf, an embryo, a root, a root tip, an anther, a flower, a bulb, a stem, a shoot, a seed, a protoplast, a cell, and a callus. 
     
     
         11 .- 12 . (canceled) 
     
     
         13 . A method of detecting in at least one onion plant a genotype associated with disease resistance or bulb color, the method comprising the step of: (i) detecting in at least one onion plant an allele of at least one polymorphic nucleic acid that is associated with disease resistance or bulb color, wherein the polymorphic nucleic acid is in or genetically linked to:
 an onion genomic region defined by loci NQ0345038 (SEQ ID NO:3) and NQ0257326 (SEQ ID NO:23) on linkage group 2 (LG2), conferring resistance to  Fusarium  basal rot (FBR);   an onion genomic region defined by loci NQ0257277 (SEQ ID NO:22) and NQ0258453 (SEQ ID NO:27) on linkage group 2 (LG2), conferring resistance to Pink Root (PR);   an onion genomic region defined by loci NQ0257220 (SEQ ID NO:26) and NQ0257692 (SEQ ID NO:29) on linkage group 2 (LG2) conferring lack of the Complimentary Pinks bulb color;   an onion genomic region defined by loci NQ0258523 (SEQ ID NO:30) and NQ0345206 (SEQ ID NO:36) on linkage group 3 (LG3), conferring resistance to  Fusarium  basal rot (FBR);   an onion genomic region defined by loci NQ0345564 (SEQ ID NO:38) and NQ0257917 (SEQ ID NO:63) on linkage group 4 (LG4), conferring resistance to  Fusarium  basal rot (FBR);   an onion genomic region defined by loci NQ0344978 (SEQ ID NO:49) and NQ0344766 (SEQ ID NO:55) on linkage group 4 (LG4), conferring resistance to Pink Root (PR);   an onion genomic region defined by loci NQ0258361 (SEQ ID NO:37) and NQ0344778 (SEQ ID NO:61) on linkage group 4 (LG4) conferring production or inhibition of bulb color;   or   an onion genomic region defined by loci NQ0257378 (SEQ ID NO:64) and NQ0345734 (SEQ ID NO:74) on linkage group 6 (LG6) conferring a red pigment bulb color.   
     
     
         14 . The method of  claim 13 , further comprising the step of: (ii) selecting at least one onion plant in which a genotype associated with disease resistance or bulb color has been detected. 
     
     
         15 . The method of  claim 13 , wherein the onion plant:
 (a) is an agronomically elite line;   (b) is a hybrid or an inbred; or   (c) is a progeny plant resulting from the cross of at least one parent plant comprising disease resistance.   
     
     
         16 .- 17 . (canceled) 
     
     
         18 . A method for producing an onion plant that comprises in its genome at least one locus associated with disease resistance or bulb color, the method comprising:
 (i) crossing a first onion plant lacking a locus associated with disease resistance or bulb color with a second onion plant comprising a locus associated with disease resistance or bulb color defined by:   an onion genomic region defined by loci NQ0345038 (SEQ ID NO:3) and NQ0257326 (SEQ ID NO:23) on linkage group 2 (LG2), conferring resistance to  Fusarium  basal rot (FBR);   an onion genomic region defined by loci NQ0257277 (SEQ ID NO:22) and NQ0258453 (SEQ ID NO:27) on linkage group 2 (LG2), conferring resistance to Pink Root (PR);   an onion genomic region defined by loci NQ0257220 (SEQ ID NO:26) and NQ0257692 (SEQ ID NO:29) on linkage group 2 (LG2) conferring lack of the Complimentary Pinks bulb color;   an onion genomic region defined by loci NQ0258523 (SEQ ID NO:30) and NQ0345206 (SEQ ID NO:36) on linkage group 3 (LG3), conferring resistance to  Fusarium  basal rot (FBR);   an onion genomic region defined by loci NQ0345564 (SEQ ID NO:38) and NQ0257917 (SEQ ID NO:63) on linkage group 4 (LG4), conferring resistance to  Fusarium  basal rot (FBR);   an onion genomic region defined by loci NQ0344978 (SEQ ID NO:49) and NQ0344766 (SEQ ID NO:55) on linkage group 4 (LG4), conferring resistance to Pink Root (PR);   an onion genomic region defined by loci NQ0258361 (SEQ ID NO:37) and NQ0344778 (SEQ ID NO:61) on linkage group 4 (LG4) conferring production or inhibition of bulb color;   or   an onion genomic region defined by loci NQ0257378 (SEQ ID NO:64) and NQ0345734 (SEQ ID NO:74) on linkage group 6 (LG6) conferring a red pigment bulb color;   (ii) detecting in progeny resulting from said crossing at least a first polymorphic locus in or genetically linked to said locus associated with disease resistance or bulb color; and   (iii) selecting an onion plant comprising said polymorphism and said locus associated with disease resistance or bulb color.   
     
     
         19 . The method of  claim 18 , further comprising the step of:
 (iv) crossing the onion plant of step (iii) with itself or another onion plant to produce a further generation.   
     
     
         20 . The method of  claim 19 , wherein steps (iii) and (iv) are repeated from about 3 times to about 10 times. 
     
     
         21 . The method of  claim 18 , wherein said onion plant:
 (a) comprises resistance to  Fusarium  basal rot (FBR) conferred by said onion genomic region defined by loci NQ0345038 (SEQ ID NO:3) and NQ0257326 (SEQ ID NO:23) on linkage group 2 (LG2), resistance to Pink Root conferred by said onion genomic region defined by loci NQ0257277 (SEQ ID NO:22) and NQ0258453 (SEQ ID NO:27) on linkage group 2 (LG2), and lack of the Complimentary Pinks bulb color conferred by said onion genomic region defined by loci NQ0257220 (SEQ ID NO:26) and NQ0257692 (SEQ ID NO:29) on linkage group 2 (LG2);   (b) is a hybrid or an inbred; or   (c) is an agronomically elite line.   
     
     
         22 .- 23 . (canceled) 
     
     
         24 . A method of onion plant breeding, the method comprising the steps of:
 (i) selecting at least a first onion plant comprising at least one allele of a polymorphic nucleic acid that is in or genetically linked to a QTL associated with disease resistance or bulb color, wherein the QTL maps to:   an onion genomic region defined by loci NQ0345038 (SEQ ID NO:3) and NQ0257326 (SEQ ID NO:23) on linkage group 2 (LG2), conferring resistance to  Fusarium  basal rot (FBR);   an onion genomic region defined by loci NQ0257277 (SEQ ID NO:22) and NQ0258453 (SEQ ID NO:27) on linkage group 2 (LG2), conferring resistance to Pink Root (PR);   an onion genomic region defined by loci NQ0257220 (SEQ ID NO:26) and NQ0257692 (SEQ ID NO:29) on linkage group 2 (LG2) conferring lack of the Complimentary Pinks bulb color;   an onion genomic region defined by loci NQ0258523 (SEQ ID NO:30) and NQ0345206 (SEQ ID NO:36) on linkage group 3 (LG3), conferring resistance to  Fusarium  basal rot (FBR);   an onion genomic region defined by loci NQ0345564 (SEQ ID NO:38) and NQ0257917 (SEQ ID NO:63) on linkage group 4 (LG4), conferring resistance to  Fusarium  basal rot (FBR);   an onion genomic region defined by loci NQ0344978 (SEQ ID NO:49) and NQ0344766 (SEQ ID NO:55) on linkage group 4 (LG4), conferring resistance to Pink Root (PR);   an onion genomic region defined by loci NQ0258361 (SEQ ID NO:37) and NQ0344778 (SEQ ID NO:61) on linkage group 4 (LG4) conferring production or inhibition of bulb color;   or   an onion genomic region defined by loci NQ0257378 (SEQ ID NO:64) and NQ0345734 (SEQ ID NO:74) on linkage group 6 (LG6) conferring a red pigment bulb color;   (ii) crossing the first onion plant with itself or a second onion plant to produce progeny onion plants comprising the QTL associated with disease resistance or bulb color.   
     
     
         25 . The method of  claim 24 , wherein at least one polymorphic nucleic acid that is genetically linked to said QTL associated with disease resistance or bulb color maps within 40 cM, 20 cM, 15 cM, 10 cM, 5 cM, or 1 cM of said QTL associated with disease resistance or bulb color. 
     
     
         26 . A method of introgressing an allele into an onion plant, the method comprising:
 (i) genotyping at least one onion plant in a population with respect to at least one polymorphic nucleic acid located in or genetically linked to:   an onion genomic region defined by loci NQ0345038 (SEQ ID NO:3) and NQ0257326 (SEQ ID NO:23) on linkage group 2 (LG2), conferring resistance to  Fusarium  basal rot (FBR);   an onion genomic region defined by loci NQ0257277 (SEQ ID NO:22) and NQ0258453 (SEQ ID NO:27) on linkage group 2 (LG2), conferring resistance to Pink Root (PR);   an onion genomic region defined by loci NQ0257220 (SEQ ID NO:26) and NQ0257692 (SEQ ID NO:29) on linkage group 2 (LG2) conferring lack of the Complimentary Pinks bulb color;   an onion genomic region defined by loci NQ0258523 (SEQ ID NO:30) and NQ0345206 (SEQ ID NO:36) on linkage group 3 (LG3), conferring resistance to  Fusarium  basal rot (FBR);   an onion genomic region defined by loci NQ0345564 (SEQ ID NO:38) and NQ0257917 (SEQ ID NO:63) on linkage group 4 (LG4), conferring resistance to  Fusarium  basal rot (FBR);   an onion genomic region defined by loci NQ0344978 (SEQ ID NO:49) and NQ0344766 (SEQ ID NO:55) on linkage group 4 (LG4), conferring resistance to Pink Root (PR);   an onion genomic region defined by loci NQ0258361 (SEQ ID NO:37) and NQ0344778 (SEQ ID NO:61) on linkage group 4 (LG4) conferring production or inhibition of bulb color;   or   an onion genomic region defined by loci NQ0257378 (SEQ ID NO:64) and NQ0345734 (SEQ ID NO:74) on linkage group 6 (LG6) conferring a red pigment bulb color;   (ii) selecting from the population at least one onion plant comprising at least one allele associated with disease resistance or bulb color.   
     
     
         27 . The method of  claim 26 , wherein the onion plant:
 (a) is an agronomically elite line; or   (b) is a hybrid or an inbred.   
     
     
         28 . (canceled) 
     
     
         29 . An onion plant obtained by the method of  claim 26 .