Yield traits for maize

Abstract

Methods for introgressing an allele of interest of a locus associated with a yield trait into Zea mays germplasm are provided. In some embodiments, the methods include providing a Zea mays plant that contains an allele of interest of a locus associated with a yield trait, wherein the locus associated with the yield trait is identifiable by PCR amplification of a Zea mays nucleic acid with a pair of oligonucleotides primers as disclosed herein, and introgressing the allele of interest into Zea mays germplasm that lacks the allele. Also provided are methods for identifying Zea mays plants that contain at least one allele associated with improved yield, improved maize plants, elite Zea mays plants, biomass produced from improved Zea mays plants, isolated and purified genetic markers, and compositions that include an amplification primer pair capable of amplifying a Zea mays nucleic acid to generate a Zea mays marker amplicon.

1 . A method for introgressing an allele of interest of a locus associated with a yield trait into  Zea mays  germplasm, the method comprising:
 (a) selecting a  Zea mays  plant that comprises an allele of interest of a locus associated with a yield trait, identifiable by PCR amplification of a  Zea mays  nucleic acid with a pair of oligonucleotides primers selected from among:
 (1) primer pair 1 represented by a primer comprising SEQ ID NO: 52 and a primer comprising SEQ ID NO: 53; 
 (2) primer pair 2 represented by a primer comprising SEQ ID NO: 57 and a primer comprising SEQ ID NO: 58; 
 (3) primer pair 3 represented by a primer comprising SEQ ID NO: 62 and a primer comprising SEQ ID NO: 63; 
 (4) primer pair 4 represented by a primer comprising SEQ ID NO: 67 and a primer comprising SEQ ID NO: 68; 
 (5) primer pair 5 represented by a primer comprising SEQ ID NO: 72 and a primer comprising SEQ ID NO: 73; 
 (6) primer pair 6 represented by a primer comprising SEQ ID NO: 77 and a primer comprising SEQ ID NO: 78; 
 (7) primer pair 7 represented by a primer comprising SEQ ID NO: 82 and a primer comprising SEQ ID NO: 83; 
 (8) primer pair 8 represented by a primer comprising SEQ ID NO: 87 and a primer comprising SEQ ID NO: 88; 
 (9) primer pair 9 represented by a primer comprising SEQ ID NO: 92 and a primer comprising SEQ ID NO: 93; 
 (10) primer pair 10 represented by a primer comprising SEQ ID NO: 97 and a primer comprising SEQ ID NO: 98; 
 (11) primer pair 11 represented by a primer comprising SEQ ID NO: 102 and a primer comprising SEQ ID NO: 103; 
 (12) primer pair 12 represented by a primer comprising SEQ ID NO: 107 and a primer comprising SEQ ID NO: 108; 
 (13) primer pair 13 represented by a primer comprising SEQ ID NO: 112 and a primer comprising SEQ ID NO: 113; 
 (14) primer pair 14 represented by a primer comprising SEQ ID NO: 117 and a primer comprising SEQ ID NO: 118; 
 (15) primer pair 15 represented by a primer comprising SEQ ID NO: 122 and a primer comprising SEQ ID NO: 123; 
 (16) primer pair 16 represented by a primer comprising SEQ ID NO: 127 and a primer comprising SEQ ID NO: 128; 
 (17) primer pair 17 represented by a primer comprising SEQ ID NO: 132 and a primer comprising SEQ ID NO: 133; 
 (18) primer pair 18 represented by a primer comprising SEQ ID NO: 137 and a primer comprising SEQ ID NO: 138; 
 (19) primer pair 19 represented by a primer comprising SEQ ID NO: 142 and a primer comprising SEQ ID NO: 143; 
 (20) primer pair 20 represented by a primer comprising SEQ ID NO: 147 and a primer comprising SEQ ID NO: 148; 
 (21) primer pair 21 represented by a primer comprising SEQ ID NO: 152 and a primer comprising SEQ ID NO: 153; 
 (22) primer pair 22 represented by a primer comprising SEQ ID NO: 157 and a primer comprising SEQ ID NO: 158; 
 (23) primer pair 23 represented by a primer comprising SEQ ID NO: 162 and a primer comprising SEQ ID NO: 163; 
 (24) primer pair 24 represented by a primer comprising SEQ ID NO: 167 and a primer comprising SEQ ID NO: 168; 
 (25) primer pair 25 represented by a primer comprising SEQ ID NO: 172 and a primer comprising SEQ ID NO: 173; 
 (26) primer pair 26 represented by a primer comprising SEQ ID NO: 177 and a primer comprising SEQ ID NO: 178; 
 (27) primer pair 27 represented by a primer comprising SEQ ID NO: 182 and a primer comprising SEQ ID NO: 183; 
 (28) primer pair 28 represented by a primer comprising SEQ ID NO: 187 and a primer comprising SEQ ID NO: 188; 
 (29) primer pair 29 represented by a primer comprising SEQ ID NO: 192 and a primer comprising SEQ ID NO: 193; 
 (30) primer pair 30 represented by a primer comprising SEQ ID NO: 197 and a primer comprising SEQ ID NO: 198; 
 (31) primer pair 31 represented by a primer comprising SEQ ID NO: 202 and a primer comprising SEQ ID NO: 203; 
 (32) primer pair 32 represented by a primer comprising SEQ ID NO: 207 and a primer comprising SEQ ID NO: 208; 
 (33) primer pair 33 represented by a primer comprising SEQ ID NO: 212 and a primer comprising SEQ ID NO: 213; 
 (34) primer pair 34 represented by a primer comprising SEQ ID NO: 217 and a primer comprising SEQ ID NO: 218; 
 (35) primer pair 35 represented by a primer comprising SEQ ID NO: 222 and a primer comprising SEQ ID NO: 223; 
 (36) primer pair 36 represented by a primer comprising SEQ ID NO: 227 and a primer comprising SEQ ID NO: 228; 
 (37) primer pair 37 represented by a primer comprising SEQ ID NO: 232 and a primer comprising SEQ ID NO: 233; 
 (38) primer pair 38 represented by a primer comprising SEQ ID NO: 237 and a primer comprising SEQ ID NO: 238; 
 (39) primer pair 39 represented by a primer comprising SEQ ID NO: 242 and a primer comprising SEQ ID NO: 243; 
 (40) primer pair 40 represented by a primer comprising SEQ ID NO: 247 and a primer comprising SEQ ID NO: 248; 
 (41) primer pair 41 represented by a primer comprising SEQ ID NO: 252 and a primer comprising SEQ ID NO: 253; 
 (42) primer pair 42 represented by a primer comprising SEQ ID NO: 257 and a primer comprising SEQ ID NO: 258; 
 (43) primer pair 43 represented by a primer comprising SEQ ID NO: 262 and a primer comprising SEQ ID NO: 263; 
 (44) primer pair 44 represented by a primer comprising SEQ ID NO: 267 and a primer comprising SEQ ID NO: 268; 
 (45) primer pair 45 represented by a primer comprising SEQ ID NO: 272 and a primer comprising SEQ ID NO: 273; 
 (46) primer pair 46 represented by a primer comprising SEQ ID NO: 277 and a primer comprising SEQ ID NO: 278; 
 (47) primer pair 47 represented by a primer comprising SEQ ID NO: 282 and a primer comprising SEQ ID NO: 283; 
 (48) primer pair 48 represented by a primer comprising SEQ ID NO: 287 and a primer comprising SEQ ID NO: 288; 
 (49) primer pair 49 represented by a primer comprising SEQ ID NO: 292 and a primer comprising SEQ ID NO: 293; 
 (50) primer pair 50 represented by a primer comprising SEQ ID NO: 297 and a primer comprising SEQ ID NO: 298; and 
 (51) primer pair 51 represented by a primer comprising SEQ ID NO: 302 and a primer comprising SEQ ID NO: 303; and 
   (b) introgressing the allele of interest into  Zea mays  germplasm that lacks the allele.   
     
     
         2 . The method of  claim 1 , wherein the allele of interest comprises any of SEQ ID NOs: 1-51, 54, 59, 64, 69, 74, 79, 84, 89, 94, 99, 104, 109, 114, 119, 124, 129, 134, 139, 144, 149, 154, 159, 164, 169, 174, 179, 184, 189, 194, 199, 204, 209, 214, 219, 224, 229, 234, 239, 244, 249, 254, 259, 264, 269, 274, 279, 284, 289, 294, 299, 304, and 307-382. 
     
     
         3 . The method of  claim 1 , wherein the allele of interest is a favorable allele that positively correlates with an improved yield-associated trait. 
     
     
         4 . The method of  claim 3 , wherein:
 (a) the yield trait is grain yield at standard moisture percentage (YGSMN), and the favorable allele comprises a nucleotide sequence comprising a G at nucleotide position 2420 of SEQ ID NO: 2; a G at nucleotide position 2709 of SEQ ID NO: 3; a T at nucleotide position 368 of SEQ ID NO: 4; a C at nucleotide position 4038 of SEQ ID NO: 5; a C at nucleotide position 4038 of SEQ ID NO: 6; an A at nucleotide position 402 of SEQ ID NO: 7; a T at nucleotide position 3050 of SEQ ID NO: 8; a C at nucleotide position 408 of SEQ ID NO: 10; a C at nucleotide position 160 of SEQ ID NO: 11; a C at nucleotide position 311 of SEQ ID NO: 12; an A at nucleotide position 338 of SEQ ID NO: 13; an A at nucleotide position 5356 of SEQ ID NO: 14; a C at nucleotide position 5371 of SEQ ID NO: 15; an A at nucleotide position 1587 of SEQ ID NO: 16; an A at nucleotide position 388 of SEQ ID NO: 17; a T at nucleotide position 494 of SEQ ID NO: 18; a T at nucleotide position 112 of SEQ ID NO: 19; a T at nucleotide position 2458 of SEQ ID NO: 20; a T at nucleotide position 4037 of SEQ ID NO: 21; a T at nucleotide position 849 of SEQ ID NO: 22; a G at nucleotide position 1032 of SEQ ID NO: 24; an A at nucleotide position 286 of SEQ ID NO: 25; an A at nucleotide position 346 of SEQ ID NO: 26; an A at nucleotide position 6968 of SEQ ID NO: 27; an A at nucleotide position 6083 of SEQ ID NO: 28; an A at nucleotide position 1729 of SEQ ID NO: 29; a C at nucleotide position 1668 of SEQ ID NO: 30; a G at nucleotide position 1255 of SEQ ID NO: 32; a C at nucleotide position 1336 of SEQ ID NO: 33; a G at nucleotide position 1486 of SEQ ID NO: 34; an A at nucleotide position 1742 of SEQ ID NO: 35; a T at nucleotide position 631 of SEQ ID NO: 37; a T at nucleotide position 3860 of SEQ ID NO: 40; an A at nucleotide position 903 of SEQ ID NO: 42; an A at nucleotide position 1795 of SEQ ID NO: 43; a T at nucleotide position 3597 of SEQ ID NO: 45; an A at nucleotide position 3611 of SEQ ID NO: 46; a C at nucleotide position 1603 of SEQ ID NO: 50; or an A at nucleotide position 2859 of SEQ ID NO: 51;   (b) the yield trait is grain moisture at harvest (GMSTP), and the favorable allele comprises a nucleotide sequence comprising a C at nucleotide position 2420 of SEQ ID NO: 2; a T at nucleotide position 2709 of SEQ ID NO: 3; a T at nucleotide position 368 of SEQ ID NO: 4; a T at nucleotide position 4038 of SEQ ID NO: 5; a T at nucleotide position 4038 of SEQ ID NO: 6; a G at nucleotide position 402 of SEQ ID NO: 7; a G at nucleotide position 3050 of SEQ ID NO: 8; a G at nucleotide position 2146 of SEQ ID NO: 9; a T at nucleotide position 408 of SEQ ID NO: 10; a G at nucleotide position 160 of SEQ ID NO: 11; a G at nucleotide position 338 of SEQ ID NO: 13; a G at nucleotide position 5356 of SEQ ID NO: 14; an A at nucleotide position 5371 of SEQ ID NO: 15; a G at nucleotide position 1587 of SEQ ID NO: 16; a G at nucleotide position 388 of SEQ ID NO: 17; a G at nucleotide position 112 of SEQ ID NO: 19; an A at nucleotide position 2458 of SEQ ID NO: 20; a C at nucleotide position 1032 of SEQ ID NO: 24; a G at nucleotide position 286 of SEQ ID NO: 25; a T at nucleotide position 6968 of SEQ ID NO: 27; a G at nucleotide position 6083 of SEQ ID NO: 28; a G at nucleotide position 1729 of SEQ ID NO: 29; an A at nucleotide position 1668 of SEQ ID NO: 30; a G at nucleotide position 5516 of SEQ ID NO: 31; a G at nucleotide position 1255 of SEQ ID NO: 32; a G at nucleotide position 1486 of SEQ ID NO: 34; an A at nucleotide position 1742 of SEQ ID NO: 35; a C at nucleotide position 2457 of SEQ ID NO: 36; a G at nucleotide position 945 of SEQ ID NO: 38; an A at nucleotide position 2378 of SEQ ID NO: 39; an A at nucleotide position 3860 of SEQ ID NO: 40; a G at nucleotide position 2519 of SEQ ID NO: 41; a G at nucleotide position 903 of SEQ ID NO: 42; a T at nucleotide position 2040 of SEQ ID NO: 44; an A at nucleotide position 3597 of SEQ ID NO: 45; an A at nucleotide position 3611 of SEQ ID NO: 46; a G at nucleotide position 131 of SEQ ID NO: 47; an A at nucleotide position 2273 of SEQ ID NO: 48; a C at nucleotide position 187 of SEQ ID NO: 49; a C at nucleotide position 1603 of SEQ ID NO: 50; or an A at nucleotide position 2859 of SEQ ID NO: 51; or   (c) the yield trait is grain weight per plot (GWTPN), and the favorable allele comprises a nucleotide sequence comprising a G at nucleotide position 1333 of SEQ ID NO: 1; a T at nucleotide position 368 of SEQ ID NO: 4; a T at nucleotide position 4038 of SEQ ID NO: 5; a C at nucleotide position 408 of SEQ ID NO: 10; an A at nucleotide position 338 of SEQ ID NO: 13; a G at nucleotide position 966 of SEQ ID NO: 23; or an A at nucleotide position 286 of SEQ ID NO: 25.   
     
     
         5 . A method for identifying a  Zea mays  plant comprising at least one allele associated with improved yield, the method comprising:
 (a) genotyping at least one  Zea mays  plant with at least one nucleic acid marker selected from among SEQ ID NOs: 1-51, 54, 59, 64, 69, 74, 79, 84, 89, 94, 99, 104, 109, 114, 119, 124, 129, 134, 139, 144, 149, 154, 159, 164, 169, 174, 179, 184, 189, 194, 199, 204, 209, 214, 219, 224, 229, 234, 239, 244, 249, 254, 259, 264, 269, 274, 279, 284, 289, 294, 299, 304, and 307-382; and   (b) selecting at least one  Zea mays  plant comprising an allele of at least one of the at least one nucleic acid marker that is associated with improved yield.   
     
     
         6 . The method of  claim 5 , wherein the allele associated with improved yield comprises a nucleotide sequence at least 85% identical to the full length nucleotide sequence set forth in any of SEQ ID NOs: 1-51, 54, 59, 64, 69, 74, 79, 84, 89, 94, 99, 104, 109, 114, 119, 124, 129, 134, 139, 144, 149, 154, 159, 164, 169, 174, 179, 184, 189, 194, 199, 204, 209, 214, 219, 224, 229, 234, 239, 244, 249, 254, 259, 264, 269, 274, 279, 284, 289, 294, 299, 304, and 307-382. 
     
     
         7 . The method of  claim 5 , wherein the allele associated with improved yield is a favorable allele that positively correlates with an improved yield trait. 
     
     
         8 . The method of  claim 7 , wherein:
 (a) the yield trait is grain yield at standard moisture percentage (YGSMN), and the favorable allele comprises a nucleotide sequence comprising a G at nucleotide position 2420 of SEQ ID NO: 2; a G at nucleotide position 2709 of SEQ ID NO: 3; a T at nucleotide position 368 of SEQ ID NO: 4; a C at nucleotide position 4038 of SEQ ID NO: 5; a C at nucleotide position 4038 of SEQ ID NO: 6; an A at nucleotide position 402 of SEQ ID NO: 7; a T at nucleotide position 3050 of SEQ ID NO: 8; a C at nucleotide position 408 of SEQ ID NO: 10; a C at nucleotide position 160 of SEQ ID NO: 11; a C at nucleotide position 311 of SEQ ID NO: 12; an A at nucleotide position 338 of SEQ ID NO: 13; an A at nucleotide position 5356 of SEQ ID NO: 14; a C at nucleotide position 5371 of SEQ ID NO: 15; an A at nucleotide position 1587 of SEQ ID NO: 16; an A at nucleotide position 388 of SEQ ID NO: 17; a T at nucleotide position 494 of SEQ ID NO: 18; a T at nucleotide position 112 of SEQ ID NO: 19; a T at nucleotide position 2458 of SEQ ID NO: 20; a T at nucleotide position 4037 of SEQ ID NO: 21; a T at nucleotide position 849 of SEQ ID NO: 22; a G at nucleotide position 1032 of SEQ ID NO: 24; an A at nucleotide position 286 of SEQ ID NO: 25; an A at nucleotide position 346 of SEQ ID NO: 26; an A at nucleotide position 6968 of SEQ ID NO: 27; an A at nucleotide position 6083 of SEQ ID NO: 28; an A at nucleotide position 1729 of SEQ ID NO: 29; a C at nucleotide position 1668 of SEQ ID NO: 30; a G at nucleotide position 1255 of SEQ ID NO: 32; a C at nucleotide position 1336 of SEQ ID NO: 33; a G at nucleotide position 1486 of SEQ ID NO: 34; an A at nucleotide position 1742 of SEQ ID NO: 35; a T at nucleotide position 631 of SEQ ID NO: 37; a T at nucleotide position 3860 of SEQ ID NO: 40; an A at nucleotide position 903 of SEQ ID NO: 42; an A at nucleotide position 1795 of SEQ ID NO: 43; a T at nucleotide position 3597 of SEQ ID NO: 45; an A at nucleotide position 3611 of SEQ ID NO: 46; a C at nucleotide position 1603 of SEQ ID NO: 50; or an A at nucleotide position 2859 of SEQ ID NO: 51;   (b) the yield trait is grain moisture at harvest (GMSTP), and the favorable allele comprises a nucleotide sequence comprising a C at nucleotide position 2420 of SEQ ID NO: 2; a T at nucleotide position 2709 of SEQ ID NO: 3; a T at nucleotide position 368 of SEQ ID NO: 4; a T at nucleotide position 4038 of SEQ ID NO: 5; a T at nucleotide position 4038 of SEQ ID NO: 6; a G at nucleotide position 402 of SEQ ID NO: 7; a G at nucleotide position 3050 of SEQ ID NO: 8; a G at nucleotide position 2146 of SEQ ID NO: 9; a T at nucleotide position 408 of SEQ ID NO: 10; a G at nucleotide position 160 of SEQ ID NO: 11; a G at nucleotide position 338 of SEQ ID NO: 13; a G at nucleotide position 5356 of SEQ ID NO: 14; an A at nucleotide position 5371 of SEQ ID NO: 15; a G at nucleotide position 1587 of SEQ ID NO: 16; a G at nucleotide position 388 of SEQ ID NO: 17; a G at nucleotide position 112 of SEQ ID NO: 19; an A at nucleotide position 2458 of SEQ ID NO: 20; a C at nucleotide position 1032 of SEQ ID NO: 24; a G at nucleotide position 286 of SEQ ID NO: 25; a T at nucleotide position 6968 of SEQ ID NO: 27; a G at nucleotide position 6083 of SEQ ID NO: 28; a G at nucleotide position 1729 of SEQ ID NO: 29; an A at nucleotide position 1668 of SEQ ID NO: 30; a G at nucleotide position 5516 of SEQ ID NO: 31; a G at nucleotide position 1255 of SEQ ID NO: 32; a G at nucleotide position 1486 of SEQ ID NO: 34; an A at nucleotide position 1742 of SEQ ID NO: 35; a C at nucleotide position 2457 of SEQ ID NO: 36; a G at nucleotide position 945 of SEQ ID NO: 38; an A at nucleotide position 2378 of SEQ ID NO: 39; an A at nucleotide position 3860 of SEQ ID NO: 40; a G at nucleotide position 2519 of SEQ ID NO: 41; a G at nucleotide position 903 of SEQ ID NO: 42; a T at nucleotide position 2040 of SEQ ID NO: 44; an A at nucleotide position 3597 of SEQ ID NO: 45; an A at nucleotide position 3611 of SEQ ID NO: 46; a G at nucleotide position 131 of SEQ ID NO: 47; an A at nucleotide position 2273 of SEQ ID NO: 48; a C at nucleotide position 187 of SEQ ID NO: 49; a C at nucleotide position 1603 of SEQ ID NO: 50; or an A at nucleotide position 2859 of SEQ ID NO: 51; or   (c) the yield trait is grain weight per plot (GWTPN), and the favorable allele comprises a nucleotide sequence comprising a G at nucleotide position 1333 of SEQ ID NO: 1; a T at nucleotide position 368 of SEQ ID NO: 4; a T at nucleotide position 4038 of SEQ ID NO: 5; a C at nucleotide position 408 of SEQ ID NO: 10; an A at nucleotide position 338 of SEQ ID NO: 13; a G at nucleotide position 966 of SEQ ID NO: 23; or an A at nucleotide position 286 of SEQ ID NO: 25.   
     
     
         9 . An improved  Zea mays  plant produced by the method of  claim 1 , or a part, seed, progeny, or tissue culture thereof. 
     
     
         10 . An elite  Zea mays  plant produced from the improved  Zea mays  plant of  claim 9 . 
     
     
         11 . Biomass produced from the improved  Zea mays  plant of  claim 10 , or from a progeny plant thereof, or from a part, seed, or tissue culture thereof. 
     
     
         12 . An isolated and purified genetic marker associated with a yield trait in  Zea mays , wherein the isolated and purified genetic marker:
 (a) comprises a nucleotide sequence as set forth in any of SEQ ID NOs: 1-382, or the reverse complement thereof, or an informative fragment thereof; and/or   (b) comprises a nucleotide sequence of an amplification product or an informative fragment thereof from a nucleic acid sample isolated from a  Zea mays  plant, wherein the amplification product is produced by amplifying a  Zea mays  nucleic acid using a pair of oligonucleotide primers selected from among SEQ ID NOs: 52 and 53, SEQ ID NOs: 57 and 58, SEQ ID NOs: 62 and 63, SEQ ID NOs: 67 and 68, SEQ ID NOs: 72 and 73, SEQ ID NOs: 77 and 78, SEQ ID NOs: 82 and 83, SEQ ID NOs: 87 and 88, SEQ ID NOs: 92 and 93, SEQ ID NOs: 97 and 98, SEQ ID NOs: 102 and 103, SEQ ID NOs: 107 and 108, SEQ ID NOs: 112 and 113, SEQ ID NOs: 117 and 118, SEQ ID NOs: 122 and 123, SEQ ID NOs: 127 and 128, SEQ ID NOs: 132 and 133, SEQ ID NOs: 137 and 138, SEQ ID NOs: 142 and 143, SEQ ID NOs: 147 and 148, SEQ ID NOs: 152 and 153, SEQ ID NOs: 157 and 158, SEQ ID NOs: 162 and 163, SEQ ID NOs: 167 and 168, SEQ ID NOs: 172 and 173, SEQ ID NOs: 177 and 178, SEQ ID NOs: 182 and 183, SEQ ID NOs: 187 and 188, SEQ ID NOs: 192 and 193, SEQ ID NOs: 197 and 198, SEQ ID NOs: 202 and 203, SEQ ID NOs: 207 and 208, SEQ ID NOs: 212 and 213, SEQ ID NOs: 217 and 218, SEQ ID NOs: 222 and 223, SEQ ID NOs: 227 and 228, SEQ ID NOs: 232 and 233, SEQ ID NOs: 237 and 238, SEQ ID NOs: 242 and 243, SEQ ID NOs: 247 and 248, SEQ ID NOs: 252 and 253, SEQ ID NOs: 257 and 258, SEQ ID NOs: 262 and 263, SEQ ID NOs: 267 and 268, SEQ ID NOs: 272 and 273, SEQ ID NOs: 277 and 278, SEQ ID NOs: 282 and 283, SEQ ID NOs: 287 and 288, SEQ ID NOs: 292 and 293, SEQ ID NOs: 297 and 298; and SEQ ID NOs: 302 and 303.   
     
     
         13 . The isolated and purified genetic marker of  claim 12 , wherein the isolated and purified genetic marker permits identification of a nucleotide in the genome of a  Zea mays  plant that corresponds to the nucleotide present at any of nucleotide position 1333 of SEQ ID NO: 1, nucleotide position 2420 of SEQ ID NO: 2, nucleotide position 2709 of SEQ ID NO: 3, nucleotide position 368 of SEQ ID NO: 4, nucleotide position 4038 of SEQ ID NO: 5, nucleotide position 4038 of SEQ ID NO: 6, nucleotide position 402 of SEQ ID NO: 7, nucleotide position 3050 of SEQ ID NO: 8, nucleotide position 2146 of SEQ ID NO: 9, nucleotide position 408 of SEQ ID NO: 10, nucleotide position 160 of SEQ ID NO: 11, nucleotide position 311 of SEQ ID NO: 12, nucleotide position 338 of SEQ ID NO: 13, nucleotide position 5356 of SEQ ID NO: 14, nucleotide position 5371 of SEQ ID NO: 15, nucleotide position 1587 of SEQ ID NO: 16, nucleotide position 388 of SEQ ID NO: 17, nucleotide position 494 of SEQ ID NO: 18, nucleotide position 112 of SEQ ID NO: 19, nucleotide position 2458 of SEQ ID NO: 20, nucleotide position 4037 of SEQ ID NO: 21, nucleotide position 849 of SEQ ID NO: 22, nucleotide position 966 of SEQ ID NO: 23; nucleotide position 1032 of SEQ ID NO: 24, nucleotide position 286 of SEQ ID NO: 25, nucleotide position 346 of SEQ ID NO: 26, nucleotide position 6968 of SEQ ID NO: 27, nucleotide position 6083 of SEQ ID NO: 28, nucleotide position 1729 of SEQ ID NO: 29, nucleotide position 1668 of SEQ ID NO: 30, nucleotide position 5516 of SEQ ID NO: 31, nucleotide position 1255 of SEQ ID NO: 32, nucleotide position 1336 of SEQ ID NO: 33, nucleotide position 1486 of SEQ ID NO: 34, nucleotide position 1742 of SEQ ID NO: 35, nucleotide position 2457 of SEQ ID NO: 36, nucleotide position 631 of SEQ ID NO: 37, nucleotide position 945 of SEQ ID NO: 38, nucleotide position 2378 of SEQ ID NO: 39, nucleotide position 3860 of SEQ ID NO: 40, nucleotide position 2519 of SEQ ID NO: 41, nucleotide position 903 of SEQ ID NO: 42, nucleotide position 1795 of SEQ ID NO: 43, nucleotide position 2040 of SEQ ID NO: 44, nucleotide position 3597 of SEQ ID NO: 45, nucleotide position 3611 of SEQ ID NO: 46, nucleotide position 131 of SEQ ID NO: 47, nucleotide position 2273 of SEQ ID NO: 48, nucleotide position 187 of SEQ ID NO: 49, nucleotide position 1603 of SEQ ID NO: 50; and nucleotide position 2859 of SEQ ID NO: 51. 
     
     
         14 . The isolated and purified genetic marker of  claim 12 , wherein the isolated and purified genetic marker further comprises a detectable moiety. 
     
     
         15 . A composition comprising an amplification primer pair capable of amplifying a  Zea mays  nucleic acid to generate a  Zea mays  marker amplicon, wherein the  Zea mays  marker amplicon corresponds to any of SEQ ID NOs: 1-51, 54, 59, 64, 69, 74, 79, 84, 89, 94, 99, 104, 109, 114, 119, 124, 129, 134, 139, 144, 149, 154, 159, 164, 169, 174, 179, 184, 189, 194, 199, 204, 209, 214, 219, 224, 229, 234, 239, 244, 249, 254, 259, 264, 269, 274, 279, 284, 289, 294, 299, 304, and 307-382. 
     
     
         16 . A method for producing an inbred  Zea mays  plant adapted for conferring, in hybrid combination with a suitable second inbred, improved yield, the method comprising:
 (a) selecting a first donor parental line possessing a desired yield trait and having at least one of improved yield loci selected from  Zea mays  loci:
 (1) ZmDWF1, mapped by one or more of the markers SEQ ID NOs: 1, 50, 51, 54, 299, 304, 307, 308, and 380-382; 
 (2) ZmZfl2, mapped by one or more of the markers SEQ ID NOs: 2-4, 59, 64, 69, and 309-312; 
 (3) ZmFea2, mapped by one or more of the markers SEQ ID NOs: 5-7, 74, 79, 89, and 313-316; 
 (4) ZmZfl1, mapped by one or more of the markers SEQ ID NOs: 8, 9, 89, 94, and 317-319; 
 (5) M1 — 8138, mapped by one or more of the markers SEQ ID NOs: 10, 99, 320, and 321; 
 (6) ZmCat3, mapped by one or more of the markers SEQ ID NOs: 11, 12, 104, 109, and 322-324; 
 (7) Zm013154, mapped by one or more of the markers SEQ ID NOs: 13, 114, 325, and 326; 
 (8) ZmSTP1, mapped by one or more of the markers SEQ ID NOs: 14, 15, 119, 124, and 327-329; 
 (9) ZmCaT, mapped by one or more of the markers SEQ ID NOs: 16, 129, 330, and 331; 
 (10) ZmAlaAT, mapped by one or more of the markers SEQ ID NOs: 17-19, 134, 139, 144, and 332-335; 
 (11) ZmD11/DWARF4L1, mapped by one or more of the markers SEQ ID NOs: 20, 21, 149, 154, and 336-338; 
 (12) ZmDWARF4, mapped by one or more of the markers SEQ ID NOs: 22, 23, 159, 164, and 339-341; 
 (13) ZmTD1, mapped by one or more of the markers SEQ ID NOs: 24-26, 169, 174, 179, and 342-345; 
 (14) ZmBT2, mapped by one or more of the markers SEQ ID NOs: 27, 28, 184, 189, and 346-348; 
 (15) ZmVrs1.1, mapped by one or more of the markers SEQ ID NOs: 29, 30, 194, 199, and 349-351; 
 (16) ZmSPS1, mapped by one or more of the markers SEQ ID NOs: 31, 204, 352, and 353; 
 (17) ZmBRI1, mapped by one or more of the markers SEQ ID NOs: 32-34, 209, 214, 219, and 354-357; 
 (18) ZmCaT2, mapped by one or more of the markers SEQ ID NOs: 35-37, 224, 229, 234, and 358-361; 
 (19) ZmCKX1, mapped by one or more of the markers SEQ ID NOs: 38-41, 239, 244, 249, 254, and 362-366; 
 (20) ZmCKX4, mapped by one or more of the markers SEQ ID NOs: 42, 259, 367, and 368; 
 (21) ZmCKX7, mapped by one or more of the markers SEQ ID NOs: 43, 44, 264, 269, and 369-371; 
 (22) ZmGW2-2, mapped by one or more of the markers SEQ ID NOs: 45, 46, 274, 279, and 372-374; 
 (23) ZmKRN1, mapped by one or more of the markers SEQ ID NOs: 47, 284, 375, and 376; and 
 (24) ZmVRS1-3 mapped by one or more of the markers SEQ ID NOs: 48, 49, 289, 294, and 377-379; 
   (b) crossing the first donor parent line with a second parental line in hybrid combination to produce a segregating plant population;   (c) screening the segregating plant population for presence of an allele associated with improved yield; and   (d) selecting plants from the population having the allele for further screening until a line is obtained which is homozygous for improved yield at sufficient loci to give improved yield in hybrid combination.   
     
     
         17 . The method of  claim 16 , wherein:
 (a) the desired yield trait is grain yield at standard moisture percentage (YGSMN), and the favorable allele comprises a nucleotide sequence comprising a G at nucleotide position 2420 of SEQ ID NO: 2; a G at nucleotide position 2709 of SEQ ID NO: 3; a T at nucleotide position 368 of SEQ ID NO: 4; a C at nucleotide position 4038 of SEQ ID NO: 5; a C at nucleotide position 4038 of SEQ ID NO: 6; an A at nucleotide position 402 of SEQ ID NO: 7; a T at nucleotide position 3050 of SEQ ID NO: 8; a C at nucleotide position 408 of SEQ ID NO: 10; a C at nucleotide position 160 of SEQ ID NO: 11; a C at nucleotide position 311 of SEQ ID NO: 12; an A at nucleotide position 338 of SEQ ID NO: 13; an A at nucleotide position 5356 of SEQ ID NO: 14; a C at nucleotide position 5371 of SEQ ID NO: 15; an A at nucleotide position 1587 of SEQ ID NO: 16; an A at nucleotide position 388 of SEQ ID NO: 17; a T at nucleotide position 494 of SEQ ID NO: 18; a T at nucleotide position 112 of SEQ ID NO: 19; a T at nucleotide position 2458 of SEQ ID NO: 20; a T at nucleotide position 4037 of SEQ ID NO: 21; a T at nucleotide position 849 of SEQ ID NO: 22; a G at nucleotide position 1032 of SEQ ID NO: 24; an A at nucleotide position 286 of SEQ ID NO: 25; an A at nucleotide position 346 of SEQ ID NO: 26; an A at nucleotide position 6968 of SEQ ID NO: 27; an A at nucleotide position 6083 of SEQ ID NO: 28; an A at nucleotide position 1729 of SEQ ID NO: 29; a C at nucleotide position 1668 of SEQ ID NO: 30; a G at nucleotide position 1255 of SEQ ID NO: 32; a C at nucleotide position 1336 of SEQ ID NO: 33; a G at nucleotide position 1486 of SEQ ID NO: 34; an A at nucleotide position 1742 of SEQ ID NO: 35; a T at nucleotide position 631 of SEQ ID NO: 37; a T at nucleotide position 3860 of SEQ ID NO: 40; an A at nucleotide position 903 of SEQ ID NO: 42; an A at nucleotide position 1795 of SEQ ID NO: 43; a T at nucleotide position 3597 of SEQ ID NO: 45; an A at nucleotide position 3611 of SEQ ID NO: 46; a C at nucleotide position 1603 of SEQ ID NO: 50; or an A at nucleotide position 2859 of SEQ ID NO: 51;   (b) the desired yield trait is grain moisture at harvest (GMSTP), and the favorable allele comprises a nucleotide sequence comprising a C at nucleotide position 2420 of SEQ ID NO: 2; a T at nucleotide position 2709 of SEQ ID NO: 3; a T at nucleotide position 368 of SEQ ID NO: 4; a T at nucleotide position 4038 of SEQ ID NO: 5; a T at nucleotide position 4038 of SEQ ID NO: 6; a G at nucleotide position 402 of SEQ ID NO: 7; a G at nucleotide position 3050 of SEQ ID NO: 8; a G at nucleotide position 2146 of SEQ ID NO: 9; a T at nucleotide position 408 of SEQ ID NO: 10; a G at nucleotide position 160 of SEQ ID NO: 11; a G at nucleotide position 338 of SEQ ID NO: 13; a G at nucleotide position 5356 of SEQ ID NO: 14; an A at nucleotide position 5371 of SEQ ID NO: 15; a G at nucleotide position 1587 of SEQ ID NO: 16; a G at nucleotide position 388 of SEQ ID NO: 17; a G at nucleotide position 112 of SEQ ID NO: 19; an A at nucleotide position 2458 of SEQ ID NO: 20; a C at nucleotide position 1032 of SEQ ID NO: 24; a G at nucleotide position 286 of SEQ ID NO: 25; a T at nucleotide position 6968 of SEQ ID NO: 27; a G at nucleotide position 6083 of SEQ ID NO: 28; a G at nucleotide position 1729 of SEQ ID NO: 29; an A at nucleotide position 1668 of SEQ ID NO: 30; a G at nucleotide position 5516 of SEQ ID NO: 31; a G at nucleotide position 1255 of SEQ ID NO: 32; a G at nucleotide position 1486 of SEQ ID NO: 34; an A at nucleotide position 1742 of SEQ ID NO: 35; a C at nucleotide position 2457 of SEQ ID NO: 36; a G at nucleotide position 945 of SEQ ID NO: 38; an A at nucleotide position 2378 of SEQ ID NO: 39; an A at nucleotide position 3860 of SEQ ID NO: 40; a G at nucleotide position 2519 of SEQ ID NO: 41; a G at nucleotide position 903 of SEQ ID NO: 42; a T at nucleotide position 2040 of SEQ ID NO: 44; an A at nucleotide position 3597 of SEQ ID NO: 45; an A at nucleotide position 3611 of SEQ ID NO: 46; a G at nucleotide position 131 of SEQ ID NO: 47; an A at nucleotide position 2273 of SEQ ID NO: 48; a C at nucleotide position 187 of SEQ ID NO: 49; a C at nucleotide position 1603 of SEQ ID NO: 50; or an A at nucleotide position 2859 of SEQ ID NO: 51; or   (c) the desired yield trait is grain weight per plot (GWTPN), and the favorable allele comprises a nucleotide sequence comprising a G at nucleotide position 1333 of SEQ ID NO: 1; a T at nucleotide position 368 of SEQ ID NO: 4; a T at nucleotide position 4038 of SEQ ID NO: 5; a C at nucleotide position 408 of SEQ ID NO: 10; an A at nucleotide position 338 of SEQ ID NO: 13; a G at nucleotide position 966 of SEQ ID NO: 23; or an A at nucleotide position 286 of SEQ ID NO: 25.   
     
     
         18 . An inbred  Zea mays  plant comprising one or more alleles associated with a desired yield trait, wherein:
 (a) the desired yield trait is grain yield at standard moisture percentage (YGSMN), and the allele of interest is selected from a nucleotide sequence comprising a G at nucleotide position 2420 of SEQ ID NO: 2; a G at nucleotide position 2709 of SEQ ID NO: 3; a T at nucleotide position 368 of SEQ ID NO: 4; a C at nucleotide position 4038 of SEQ ID NO: 5; a C at nucleotide position 4038 of SEQ ID NO: 6; an A at nucleotide position 402 of SEQ ID NO: 7; a T at nucleotide position 3050 of SEQ ID NO: 8; a C at nucleotide position 408 of SEQ ID NO: 10; a C at nucleotide position 160 of SEQ ID NO: 11; a C at nucleotide position 311 of SEQ ID NO: 12; an A at nucleotide position 338 of SEQ ID NO: 13; an A at nucleotide position 5356 of SEQ ID NO: 14; a C at nucleotide position 5371 of SEQ ID NO: 15; an A at nucleotide position 1587 of SEQ ID NO: 16; an A at nucleotide position 388 of SEQ ID NO: 17; a T at nucleotide position 494 of SEQ ID NO: 18; a T at nucleotide position 112 of SEQ ID NO: 19; a T at nucleotide position 2458 of SEQ ID NO: 20; a T at nucleotide position 4037 of SEQ ID NO: 21; a T at nucleotide position 849 of SEQ ID NO: 22; a G at nucleotide position 1032 of SEQ ID NO: 24; an A at nucleotide position 286 of SEQ ID NO: 25; an A at nucleotide position 346 of SEQ ID NO: 26; an A at nucleotide position 6968 of SEQ ID NO: 27; an A at nucleotide position 6083 of SEQ ID NO: 28; an A at nucleotide position 1729 of SEQ ID NO: 29; a C at nucleotide position 1668 of SEQ ID NO: 30; a G at nucleotide position 1255 of SEQ ID NO: 32; a C at nucleotide position 1336 of SEQ ID NO: 33; a G at nucleotide position 1486 of SEQ ID NO: 34; an A at nucleotide position 1742 of SEQ ID NO: 35; a T at nucleotide position 631 of SEQ ID NO: 37; a T at nucleotide position 3860 of SEQ ID NO: 40; an A at nucleotide position 903 of SEQ ID NO: 42; an A at nucleotide position 1795 of SEQ ID NO: 43; a T at nucleotide position 3597 of SEQ ID NO: 45; an A at nucleotide position 3611 of SEQ ID NO: 46; a C at nucleotide position 1603 of SEQ ID NO: 50; and an A at nucleotide position 2859 of SEQ ID NO: 51;   (b) the desired yield trait is grain moisture at harvest (GMSTP), and the allele of interest is selected from a nucleotide sequence comprising a C at nucleotide position 2420 of SEQ ID NO: 2; a T at nucleotide position 2709 of SEQ ID NO: 3; a T at nucleotide position 368 of SEQ ID NO: 4; a T at nucleotide position 4038 of SEQ ID NO: 5; a T at nucleotide position 4038 of SEQ ID NO: 6; a G at nucleotide position 402 of SEQ ID NO: 7; a G at nucleotide position 3050 of SEQ ID NO: 8; a G at nucleotide position 2146 of SEQ ID NO: 9; a T at nucleotide position 408 of SEQ ID NO: 10; a G at nucleotide position 160 of SEQ ID NO: 11; a G at nucleotide position 338 of SEQ ID NO: 13; a G at nucleotide position 5356 of SEQ ID NO: 14; an A at nucleotide position 5371 of SEQ ID NO: 15; a G at nucleotide position 1587 of SEQ ID NO: 16; a G at nucleotide position 388 of SEQ ID NO: 17; a G at nucleotide position 112 of SEQ ID NO: 19; an A at nucleotide position 2458 of SEQ ID NO: 20; a C at nucleotide position 1032 of SEQ ID NO: 24; a G at nucleotide position 286 of SEQ ID NO: 25; a T at nucleotide position 6968 of SEQ ID NO: 27; a G at nucleotide position 6083 of SEQ ID NO: 28; a G at nucleotide position 1729 of SEQ ID NO: 29; an A at nucleotide position 1668 of SEQ ID NO: 30; a G at nucleotide position 5516 of SEQ ID NO: 31; a G at nucleotide position 1255 of SEQ ID NO: 32; a G at nucleotide position 1486 of SEQ ID NO: 34; an A at nucleotide position 1742 of SEQ ID NO: 35; a C at nucleotide position 2457 of SEQ ID NO: 36; a G at nucleotide position 945 of SEQ ID NO: 38; an A at nucleotide position 2378 of SEQ ID NO: 39; an A at nucleotide position 3860 of SEQ ID NO: 40; a G at nucleotide position 2519 of SEQ ID NO: 41; a G at nucleotide position 903 of SEQ ID NO: 42; a T at nucleotide position 2040 of SEQ ID NO: 44; an A at nucleotide position 3597 of SEQ ID NO: 45; an A at nucleotide position 3611 of SEQ ID NO: 46; a G at nucleotide position 131 of SEQ ID NO: 47; an A at nucleotide position 2273 of SEQ ID NO: 48; a C at nucleotide position 187 of SEQ ID NO: 49; a C at nucleotide position 1603 of SEQ ID NO: 50; and an A at nucleotide position 2859 of SEQ ID NO: 51; and/or   (c) the desired yield trait is grain weight per plot (GWTPN), and the allele of interest is selected from a nucleotide sequence comprising a G at nucleotide position 1333 of SEQ ID NO: 1; a T at nucleotide position 368 of SEQ ID NO: 4; a T at nucleotide position 4038 of SEQ ID NO: 5; a C at nucleotide position 408 of SEQ ID NO: 10; an A at nucleotide position 338 of SEQ ID NO: 13; a G at nucleotide position 966 of SEQ ID NO: 23; or an A at nucleotide position 286 of SEQ ID NO: 25.