Soybean plants having superior agronomic performance and methods for their production

Abstract

This invention provides compositions including favorable alleles of marker loci associated with genetic elements contributing to superior agronomic performance. Also provided are markers for identifying favorable alleles of marker loci associated with genetic elements involved in superior agronomic performance, as well as methods employing the markers.

What is claimed is: 
     
         1 . A method of identifying a soybean subline with increased yield, the method comprising: determining in a genome of each of a plurality of progeny of a progenitor soybean, at least one allelic form of between about 10% and about 100% of the chromosome segments each comprising a genetic element contributing to increased yield and each comprising or proximal to a marker locus selected from the set of marker loci consisting of: Satt684, Satt165, Satt042, Satt364, Satt454, Satt526, Satt300, Satt591, Satt155, Satt385, Satt225, Satt236, Satt511, P12390B-1, Satt480, Satt632-TB, Satt233, Satt327, Satt329, Satt508, P10635A-1, Satt409, Satt228, Satt429, Satt426, Satt509, SAT — 261, Satt197, Satt519, Satt597, SCT — 026, Satt415, Satt583, Satt430, P12198A-1, P8584A-1, Satt359, P10648A-1, P12105A-1, P10641A-1, Satt168, Satt556, Satt272, Satt020, Satt066, Satt534, P10638B-2, Satt399, Satt361, P10639A-1, Satt661-TB, Satt190, SAT — 311-DB, Satt338, Satt227, Satt640-TB, Satt422, Satt457, Satt557, Satt319, SAT — 142-DB, Satt460, P13073A-1, Satt307, SCT-028, Satt433, Satt357, Satt321, Satt267, Satt383, Satt295, Satt203, Satt507, SAT — 110, P10620A-1, Satt129, Satt147, Satt216, SAT — 351, P10621B-2, Satt701, Satt634, Satt558, Satt266, Satt282, Satt537, Satt506, Satt546, P13072A-1, Satt582, Satt389, Satt461, Satt311, Satt514, Satt464, Satt662, Satt543, Satt186, Satt413, Satt672, P13074A-1, P10624A-1, Satt573, Satt598, Satt204, Satt263, Satt491, Satt602, Satt151, Satt355, Satt452, SAT — 273-DB, Satt146, Satt193, Satt569, Satt343, Satt586, Satt040, Satt423, Satt348, Satt595, P10782A-1, P3436A-1, P10598A-1, Satt334, Satt510, Satt144, Satt522, P9026A-1, P10646A-1, P5219A-1, P7659A-2, Satt570, Satt356, Satt130, Satt115, Satt594, Satt533, Satt303, Satt352, Satt566, Satt199, Satt503, Satt517, Satt191, SAT — 117, Satt353, Satt442, Satt279, Satt314, Satt142, Satt181, Satt367, Satt127, SCTT012, Satt270, Satt292, Satt440, P10640A-1, Satt249, SCT — 065, Satt596, Satt280, Satt406, Satt380, Satt183, Satt529, Satt431, Satt242, Satt102, Satt441, Satt544, Satt617, Satt240, P10618A-1, Satt475, Satt196, SAT — 301, Satt523, Satt418, Satt398, Satt497, Satt284, Satt166, Satt448, Satt373, Satt513, P12394A-1, Satt590, Satt567, Satt220, Satt536, Satt175, Satt677, Satt680, P10615A-1, Satt551, Satt250, Satt346, Satt336, SAT — 330-DB, P13069A-1, P5467A-1, P5467A-2, Satt584, SAT — 084, P3050A-2, SAT — 275-DB, Satt387, Satt549, Satt660, Satt339, Satt255, Satt257, Satt358, P12396A-1, Satt487, Satt259, Satt347, Satt420, Satt576, Satt550, Satt633, Satt262, Satt473, Satt477, Satt581, P11070A-1, Satt153, Satt243, P8230A-1, P10623A-1, P10632A-1, P10793A-1, P12391A-1, P13560A-1, P13561A-1, P2481A-1, Satt040, Satt108, Satt109, Satt111, Satt176, Satt219, Satt299, and Satt512; wherein the favorable allelic form of at least one chromosome segment is determined by: a) identifying at least one polymorphic marker locus selected from the set in a plurality of sublines of progeny of a progenitor soybean; b) assessing yield in at least two sublines of progeny, which sublines of progeny have different allelic forms of at least one marker locus; and, c) identifying the subline of progeny with increased yield relative to the progenitor soybean; thereby identifying a subline with increased yield. 
     
     
         2 . The method of  claim 1 , wherein the at least two sublines of progeny are near isogenic sublines. 
     
     
         3 . The method of  claim 1 , wherein the at least two sublines of progeny are random sublines. 
     
     
         4 . The method of  claim 1 , wherein the plurality of progeny are obtained by selfing a progenitor soybean. 
     
     
         5 . The method of  claim 1 , wherein the plurality of progeny are obtained by crossing a first progenitor soybean and a second progenitor soybean. 
     
     
         6 . The method of  claim 5 , wherein a first progenitor soybean comprising a strain of elite germplasm is crossed with a second progenitor soybean comprising a different strain of elite germplasm to generate a population of soybean plants from which the progeny is selected. 
     
     
         7 . The method of  claim 5 , wherein a first progenitor soybean comprising a strain of elite germplasm is crossed with a second progenitor soybean comprising a strain of exotic germplasm to generate a population of soybean plants from which the progeny is selected. 
     
     
         8 . The method of  claim 6 , wherein the elite strain of germplasm is selected from the group consisting of: 90A07, 90B11, 90B31, 90B43, 90B72, 90B73, 91B01, 94B53, 94B54, 94B73, 95B32, 95B33, 95B34, 95B53, 95B95, 95B96, 95B97, 96B21, 96B51, 97B52, 97B61, BEDFORD, CX105, CX232, CX253, CX289, CX394C, CX469C, ESSEX, EX04C00, FORREST, HS93-4118, HUTCHESON, JIM, KORADA, PHARAOH, S0066, S0880, S1990, S19T9, S20F8, S25J5, S32Z3, S33N1, S38T8, S3911, S4260, S42H1, S43B5, S5960, S6262, ST0653, ST1073, ST1090, ST1570, ST1690, ST1970, ST2250, ST2488, ST2660, ST2686, ST2688, ST2788, ST2870, ST3171, ST3630, ST3660, ST3870, ST3883, TRACY, TRAILL, and YOUNG. 
     
     
         9 . The method of  claim 1 , further comprising selecting at least one plant of the identified soybean subline. 
     
     
         10 . The method of  claim 9 , wherein the selected soybean plant comprises a whole plant, a plant organ, a plant seed, a plant cell or a plant tissue culture. 
     
     
         11 . The method of  claim 9 , wherein the selected soybean plant or a progeny thereof is crossed with a second soybean plant, which second soybean plant lacks the determined alleles of marker loci or the determined allelic forms of the plurality of chromosome segments. 
     
     
         12 . A plant comprising in its genome a set of genetic elements related to increased yield, wherein said set of genetic elements comprises one or more genetic elements proximal to each of at least 10% of the markers selected from the group consisting of:
 Satt684, Satt165, Satt042, Satt364, Satt454, Satt526, Satt300, Satt591, Satt155, Satt385, Satt225, Satt236, Satt511, P12390B-1, Satt480, Satt632-TB, Satt233, Satt327, Satt329, Satt508, P10635A-1, Satt409, Satt228, Satt429, Satt426, Satt509, SAT — 261, Satt197, Satt519, Satt597, SCT — 026, Satt415, Satt583, Satt430, P12198A-1, P8584A-1, Satt359, P10648A-1, P12105A-1, P10641A-1, Satt168, Satt556, Satt272, Satt020, Satt066, Satt534, P10638B-2, Satt399, Satt361, P10639A-1, Satt661-TB, Satt190, SAT — 311-DB, Satt338, Satt227, Satt640-TB, Satt422, Satt457, Satt557, Satt319, SAT — 142-DB, Satt460, P13073A-1, Satt307, SCT — 028, Satt433, Satt357, Satt321, Satt267, Satt383, Satt295, Satt203, Satt507, SAT — 110, P10620A-1, Satt129, Satt147, Satt216, SAT — 351, P10621B-2, Satt701, Satt634, Satt558, Satt266, Satt282, Satt537, Satt506, Satt546, P13072A-1, Satt582, Satt389, Satt461, Satt311, Satt514, Satt464, Satt662, Satt543, Satt186, Satt413, Satt672, P13074A-1, P10624A-1, Satt573, Satt598, Satt204, Satt263, Satt491, Satt602, Satt151, Satt355, Satt452, SAT — 273-DB, Satt146, Satt193, Satt569, Satt343, Satt586, Satt040, Satt423, Satt348, Satt595, P10782A-1, P3436A-1, P10598A-1, Satt334, Satt510, Satt144, Satt522, P9026A-1, P10646A-1, P5219A-1, P7659A-2, Satt570, Satt356, Satt130, Satt115, Satt594, Satt533, Satt303, Satt352, Satt566, Satt199, Satt503, Satt517, Satt191, SAT — 117, Satt353, Satt442, Satt279, Satt314, Satt142, Satt181, Satt367, Satt127, SCTT012, Satt270, Satt292, Satt440, P10640A-1, Satt249, SCT — 065, Satt596, Satt280, Satt406, Satt380, Satt183, Satt529, Satt431, Satt242, Satt102, Satt441, Satt544, Satt617, Satt240, P10618A-1, Satt475, Satt196, SAT — 301, Satt523, Satt418, Satt398, Satt497, Satt284, Satt166, Satt448, Satt373, Satt513, P12394A-1, Satt590, Satt567, Satt220, Satt536, Satt175, Satt677, Satt680, P10615A-1, Satt551, Satt250, Satt346, Satt336, SAT — 330-DB, P13069A-1, P5467A-1, P5467A-2, Satt584, SAT — 084, P3050A-2, SAT — 275-DB, Satt387, Satt549, Satt660, Satt339, Satt255, Satt257, Satt358, P12396A-1, Satt487, Satt259, Satt347, Satt420, Satt576, Satt550, Satt633, Satt262, Satt473, Satt477, Satt581, P11070A-1, Satt153, Satt243, P8230A-1, P10623A-1, P10632A-1, P10793A-1, P12391A-1, P13560A-1, P13561A-1, P2481A-1, Satt040, Satt108, Satt109, Satt111, Satt176, Satt219, Satt299, and Satt512.   
     
     
         13 . The plant of  claim 12 , wherein said set of genetic elements comprises one or more genetic elements proximal to each of at least 50% of the markers selected from the group consisting of:
 Satt684, Satt165, Satt042, Satt364, Satt454, Satt526, Satt300, Satt591, Satt155, Satt385, Satt225, Satt236, Satt511, P12390B-1, Satt480, Satt632-TB, Satt233, Satt327, Satt329, Satt508, P10635A-1, Satt409, Satt228, Satt429, Satt426, Satt509, SAT — 261, Satt197, Satt519, Satt597, SCT — 026, Satt415, Satt583, Satt430, P12198A-1, P8584A-1, Satt359, P10648A-1, P12105A-1, P10641A-1, Satt168, Satt556, Satt272, Satt020, Satt066, Satt534, P10638B-2, Satt399, Satt361, P10639A-1, Satt661-TB, Satt190, SAT — 311-DB, Satt338, Satt227, Satt640-TB, Satt422, Satt457, Satt557, Satt319, SAT — 142-DB, Satt460, P13073A-1, Satt307, SCT — 028, Satt433, Satt357, Satt321, Satt267, Satt383, Satt295, Satt203, Satt507, SAT — 110, P10620A-1, Satt129, Satt147, Satt216, SAT — 351, P10621B-2, Satt701, Satt634, Satt558, Satt266, Satt282, Satt537, Satt506, Satt546, P13072A-1, Satt582, Satt389, Satt461, Satt311, Satt514, Satt464, Satt662, Satt543, Satt186, Satt413, Satt672, P13074A-1, P10624A-1, Satt573, Satt598, Satt204, Satt263, Satt491, Satt602, Satt151, Satt355, Satt452, SAT — 273-DB, Satt146, Satt193, Satt569, Satt343, Satt586, Satt040, Satt423, Satt348, Satt595, P10782A-1, P3436A-1, P10598A-1, Satt334, Satt510, Satt144, Satt522, P9026A-1, P10646A-1, P5219A-1, P7659A-2, Satt570, Satt356, Satt130, Satt115, Satt594, Satt533, Satt303, Satt352, Satt566, Satt199, Satt503, Satt517, Satt191, SAT — 117, Satt353, Satt442, Satt279, Satt314, Satt142, Satt181, Satt367, Satt127, SCTT012, Satt270, Satt292, Satt440, P10640A-1, Satt249, SCT — 065, Satt596, Satt280, Satt406, Satt380, Satt183, Satt529, Satt431, Satt242, Satt102, Satt441, Satt544, Satt617, Satt240, P10618A-1, Satt475, Satt196, SAT — 301, Satt523, Satt418, Satt398, Satt497, Satt284, Satt166, Satt448, Satt373, Satt513, P12394A-1, Satt590, Satt567, Satt220, Satt536, Satt175, Satt677, Satt680, P10615A-1, Satt551, Satt250, Satt346, Satt336, SAT — 330-DB, P13069A-1, P5467A-1, P5467A-2, Satt584, SAT — 084, P3050A-2, SAT — 275-DB, Satt387, Satt549, Satt660, Satt339, Satt255, Satt257, Satt358, P12396A-1, Satt487, Satt259, Satt347, Satt420, Satt576, Satt550, Satt633, Satt262, Satt473, Satt477, Satt581, P11070A-1, Satt153, Satt243, P8230A-1, P10623A-1, P10632A-1, P10793A-1, P12391A-1, P13560A-1, P13561A-1, P2481A-1, Satt040, Satt108, Satt109, Satt111, Satt176, Satt219, Satt299, and Satt512.   
     
     
         14 . The plant of  claim 12 , wherein said set of genetic elements comprises one or more genetic elements proximal to each of at least 10% of the markers selected from the group consisting of:
 Satt642, Satt042, Satt364, Satt454, Satt526, Satt300, Satt591, Satt155, Satt385, Satt511, P12390B-1, Satt632-TB, Satt429, SAT — 261, Satt197, P10641A-1, Satt556, Satt534, P10638B-2, Satt399, Satt361, P10639A-1, Satt661-TB, Satt190, SAT — 311-DB, Satt338, Satt640-TB, Satt557, Satt319, SAT — 142-DB, Satt460, Satt433, Satt357, Satt321, Satt295, Satt203, Satt507, Satt129, Satt147, SAT — 351, P10621B-2, Satt558, Satt701, Satt634, Satt582, Satt389, Satt464, Satt662, Satt672, Satt573, Satt598, Satt263, Satt602, Satt151, SAT — 273-DB, Satt146, Satt193, Satt569, Satt176, Satt343, Satt586, Satt040, Satt595, P10782A-1, Satt334, Satt144, Satt522, Satt570, Satt356, Satt533, Satt199, Satt517, Satt191, SAT — 117, Satt279, Satt181, Satt127, Satt270, Satt292, SAT — 065, Satt596, Satt406, Satt380, Satt183, Satt529, Satt242, Satt617, Satt240, SAT — 301, Satt418, Satt398, Satt497, Satt166, Satt448, Satt373, Satt513, P12394A-1, Satt536, Satt175, Satt677, Satt680, P10615A-1, Satt551, Satt346, Satt336, SAT — 330-DB, P13069A-1, P5467A-1, P5467A-2, SAT — 084, SAT — 275-DB, Satt660, Satt339, P12396A-1, Satt358, Satt487, Satt259, Satt420, Satt576, Satt633, Satt477, Satt581, Satt153, Satt243, P10793A-1, P12391A-1, P12392A-1, P13560A-1, P13561A-1, Satt040, Satt111, Satt176, Satt219, and Satt299.   
     
     
         15 . The plant of  claim 12 , wherein said set of genetic elements comprises one or more genetic elements proximal to each of at least 10% of the markers selected from the group consisting of:
 Satt684, Satt042, Satt364, Satt454, Satt526, Satt300, Satt591, Satt155, Satt385, Satt632-TB, Satt429, SAT — 261, P10641A-1, Satt556, P10638B-2, Satt399, Satt361, Satt661-TB, Satt190, SAT — 311-DB, Satt338, Satt640-TB, Satt557, Satt319, SAT — 142-DB, Satt321, Satt203, Satt129, Satt147, SAT — 351, P10621B-2, Satt701, Satt634, Satt582, Satt389, Satt464, Satt662, Satt672, Satt573, Satt598, Satt263, Satt151, SAT — 273-DB, Satt146, Satt193, Satt569, Satt343, Satt586, Satt040, Satt595, Satt334, Satt144, Satt522, Satt570, Satt356, Satt199, Satt517, Satt191, SAT — 117, Satt279, Satt181, Satt127, Satt270, Satt292, Sat — 065, Satt596, Satt406, Satt380, Satt183, Satt529, Satt242, Satt617, Satt240, SAT — 301, Satt418, Satt398, Satt497, Satt166, Satt448, Satt373, Satt513, P12394A-1, Satt536, Satt175, Satt677, Satt680, P10615A-1, Satt551, SAT — 330-DB, P13069A-1, P5467A-1, P5467A-2, SAT — 084, SAT — 275-DB, Satt660, Satt339, Satt358, Satt487, Satt420, Satt576, Satt633, Satt581, Satt153, Satt243, P10793A-1, P13560A-1, P13561A-1, Satt111, Satt219, and Satt299.   
     
     
         16 . The plant of  claim 12 , wherein said set of genetic elements comprises one or more genetic elements proximal to each of at least 50% of the markers selected from the group consisting of:
 Satt684, Satt526, Satt591, Satt385, Satt632-TB, Satt429, SAT — 261, P10641A-1, Satt556, P10638B-2, Satt190, SAT — 311-DB, Satt338, Satt640-TB, Satt557, SAT — 142-DB, Satt321, Satt203, Satt129, SAT — 351, Satt701, Satt582, Satt389, Satt464, Satt672, Satt598, Satt343, Satt595, Satt334, Satt144, Satt522, Satt570, Satt356, Satt199, Sat — 117, Satt279, Satt181, Satt127, Satt270, Satt292, Sat — 065, Satt529, Satt242, Satt617, SAT — 301, Satt398, Satt497, Satt166, Satt373, Satt680, P10615A-1, SAT — 330-DB, P13069A-1, SAT — 275-DB, Satt339, Satt487, Satt420, Satt58, 1 and Satt153.   
     
     
         17 . The plant of  claim 12 , wherein said set of genetic elements comprises one or more genetic elements proximal to each of the markers:
 Satt526, Satt591, Satt429, SAT- — 261, P10641A-1, Satt190, Satt557, SAT — 142-DB, Satt129, SAT — 351, Satt464, Satt343, Satt595, Satt570, Satt181, Satt127, Satt270, Sat — 065, Satt529, Satt242, Satt398, Satt166, Satt373, Satt680, SAT — 330-DB, P13069A-1, Satt339, Satt487, Satt581, and Satt153.   
     
     
         18 . The plant of  claim 12 , wherein the plant is a soybean line or soybean variety. 
     
     
         19 . The plant of  claim 17 , wherein the plant is a soybean line or soybean variety. 
     
     
         20 . The plant of  claim 12 , wherein the plant comprises an elite soybean strain or an exotic soybean strain. 
     
     
         21 . The plant of  claim 17 , wherein the plant comprises an elite soybean strain or an exotic soybean strain. 
     
     
         22 . A field comprising a plurality of plants of  claim 12 . 
     
     
         23 . A field comprising a plurality of plants of  claim 17 . 
     
     
         24 . A seed of the plant of  claim 12 . 
     
     
         25 . A seed of the plant of  claim 17 . 
     
     
         26 . A method of producing a plant having increased yield, the method comprising planting the seed of  claim 24  in soil and growing a plant therefrom. 
     
     
         27 . A method of producing a plant having increased yield, the method comprising planting the seed of  claim 25  in soil and growing a plant therefrom.