Complementary genetic and genomic approaches help characterize the linkage group I seed protein QTL in soybean.
BACKGROUND
The nutritional and economic value of many crops is effectively a function of seed protein and oil content. Insight into the genetic and molecular control mechanisms involved in the deposition of these constituents in the developing seed is needed to guide crop improvement. A quantitative trait locus (QTL) on Linkage Group I (LG I) of soybean (Glycine max (L.) Merrill) has a striking effect on seed protein content.


RESULTS
A soybean near-isogenic line (NIL) pair contrasting in seed protein and differing in an introgressed genomic segment containing the LG I protein QTL was used as a resource to demarcate the QTL region and to study variation in transcript abundance in developing seed. The LG I QTL region was delineated to less than 8.4 Mbp of genomic sequence on chromosome 20. Using Affymetrix Soy GeneChip and high-throughput Illumina whole transcriptome sequencing platforms, 13 genes displaying significant seed transcript accumulation differences between NILs were identified that mapped to the 8.4 Mbp LG I protein QTL region.


CONCLUSIONS
This study identifies gene candidates at the LG I protein QTL for potential involvement in the regulation of protein content in the soybean seed. The results demonstrate the power of complementary approaches to characterize contrasting NILs and provide genome-wide transcriptome insight towards understanding seed biology and the soybean genome.
Bolon
Yung-Tsi
YT
United States Department of Agriculture-Agricultural Research Service, Plant Research Unit, St Paul, MN 55108, USA.
Joseph
Bindu
B
Cannon
Steven B
SB
Graham
Michelle A
MA
Diers
Brian W
BW
Farmer
Andrew D
AD
May
Gregory D
GD
Muehlbauer
Gary J
GJ
Specht
James E
JE
Tu
Zheng Jin
ZJ
Weeks
Nathan
N
Xu
Wayne W
WW
Shoemaker
Randy C
RC
Vance
Carroll P
CP
D018744:DNA, Plant / Q000235:genetics; D020869:Gene Expression Profiling; D018745:Genome, Plant; D023281:Genomics / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis; D020161:Physical Chromosome Mapping; D010938:Plant Oils / Q000032:analysis; D011110:Polymorphism, Genetic; D040641:Quantitative Trait Loci; D055314:Seed Storage Proteins / Q000235:genetics*; D012639:Seeds / Q000235:genetics; D017422:Sequence Analysis, DNA; D013025:Glycine max / Q000235:genetics*
D018744:DNA, Plant; D010938:Plant Oils; D055314:Seed Storage Proteins