Genetic separation of southern and northern soybean breeding programs in North America and their associated allelic variation at four maturity loci

Molecular Breeding, Jan 2017

North American soybean breeders have successfully developed a large number of elite cultivars with diverse maturity groups (MG) from a small number of ancestral landraces. To understand molecular and genetic basis underlying the large variation in their maturity and flowering times, we integrated pedigree and maturity data of 166 cultivars representing North American soybean breeding. Network analysis and visualization of their pedigree relationships revealed a clear separation of southern and northern soybean breeding programs, suggesting that little genetic exchange occurred between northern (MG 0–IV) and southern cultivars (MG V–VIII). We also analyzed the transcript sequence and expression levels of four major maturity genes (E1 to E4) and revealed their allelic variants in 75 major ancestral landraces and milestone cultivars. We observed that e1-as was the predominant e mutant allele in northern genotypes, followed by e2 and e3. There was no allelic variation at E4. Transcript accumulation of the e2 mutant allele was significantly reduced, which might be caused by its premature stop codon triggering the nonsense-mediated mRNA decay pathway. The large DNA deletion generating the e3 mutant allele also created a gene fusion transcript. The e alleles found in milestone cultivars were traced through pedigrees to their ancestral landraces and geographic origins. Our analysis revealed an approximate correlation between dysfunctional alleles and maturity groups for most of the 75 cultivars. However, single e mutant alleles and their combinations were not sufficient to fully explain their maturity diversity, suggesting that additional genes/alleles are likely involved in regulating maturity time.

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Genetic separation of southern and northern soybean breeding programs in North America and their associated allelic variation at four maturity loci

Mol Breeding Genetic separation of southern and northern soybean breeding programs in North America and their associated allelic variation at four maturity loci Goettel Wolfgang Yong-qiang Charles An 0 US Department of Agriculture, Agricultural Research Service, Midwest Area, Plant Genetics Research Unit at Donald Danforth Plant Science Center , 975 N Warson Rd, St. Louis, MO 63132 , USA North American soybean breeders have successfully developed a large number of elite cultivars with diverse maturity groups (MG) from a small number of ancestral landraces. To understand molecular and genetic basis underlying the large variation in their maturity and flowering times, we integrated pedigree and maturity data of 166 cultivars representing North American soybean breeding. Network analysis and visualization of their pedigree relationships revealed a clear separation of southern and northern soybean breeding programs, suggesting that little genetic exchange occurred between northern (MG 0-IV) and southern cultivars (MG VVIII). We also analyzed the transcript sequence and expression levels of four major maturity genes (E1 to E4) and revealed their allelic variants in 75 major ancestral landraces and milestone cultivars. We observed that e1-as was the predominant e mutant allele in northern genotypes, followed by e2 and e3. There was no allelic variation at E4. Transcript accumulation of the e2 mutant allele was significantly reduced, which might be caused by its premature stop codon triggering the nonsensemediated mRNA decay pathway. The large DNA deletion generating the e3 mutant allele also created a gene fusion transcript. The e alleles found in milestone cultivars were traced through pedigrees to their ancestral landraces and geographic origins. Our analysis revealed an approximate correlation between dysfunctional alleles and maturity groups for most of the 75 cultivars. However, single e mutant alleles and their combinations were not sufficient to fully explain their maturity diversity, suggesting that additional genes/alleles are likely involved in regulating maturity time. Soybean; breeding history; Pedigree; Breeding; Network; E genes and maturity - Soybean (Glycine max (L.) Merrill) is a photoperiodsensitive plant that flowers in response to shorter day length. Soybean cultivars have to acquire photoperiodic insensitivity to flower and produce seeds at higher latitudes (Xu et al. 2013) . Soybean was domesticated from its wild relative Glycine soja in East Asia several thousand years ago. In contrast, soybean has a rather short history in North America. Soybean was only introduced to North America in the seventeenth century and was mostly grown as a forage crop until the 1920s. The first modern soybean cultivar developed by hybridization in North American breeding programs was released in 1939 (Bernard et al. 1988) . The transition from selecting landraces to breeding cultivars resulted in a significant genetic improvement of soybean cultivars (Rincker et al. 2014) . During soybean domestication and breeding, soybean cultivars with a wide range of flowering and maturity time were developed. Current soybean cultivars have been bred to grow in latitudes ranging from the equator to 50° N and higher (Tsubokura et al. 2013) . In general, a given cultivar is developed for maximum yield potential within a specific latitude range. Cultivars are assigned to specific maturity groups ranging from 000 to X, which indicate their preferred latitudinal or geographic zones in North America from Southern Canada (000) to Mexico and the Caribbean Islands (X). Cultivars with a wide range of maturity groups have been bred in North America since the first soybean hybrid cultivar was released. To associate soybean maturity with North American soybean pedigrees, we compiled pedigree and maturity group data of 166 soybean genotypes through comprehensive database and literature searches. These genotypes include landrace and milestone cultivars that represent 90 years of North American soybean breeding. The cultivars belong to diverse maturity groups (MG) from 0 to VIII. The pedigree data were analyzed and visualized using a networking approach (Shannon et al. 2003) (Fig. 1). A total of 166 soybean cultivars were represented as nodes and 274 parent-offspring relationships were represented as directed edges pointing from parental to progeny cultivars. The soybean cultivars grouped into two distinct clusters (Fig. 1). The smaller cluster contained 55 cultivars and 85 parent-offspring connections, and the larger cluster consisted of 110 cultivars with 180 parent-offspring relations. Only eight parent-offspring relations bridged the two clusters. Interestingly, the two clusters were defined by cultivars of either northern (MG 0–IV) or southern (MG V to VIII) maturity groups. Cultivars in the smaller cluster exclusively belonged to maturity groups 0–IV, while cultivars in the larger cluster predominantly belonged to mat (...truncated)


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Goettel Wolfgang, Yong-qiang Charles An. Genetic separation of southern and northern soybean breeding programs in North America and their associated allelic variation at four maturity loci, Molecular Breeding, 2017, pp. 8, Volume 37, Issue 1, DOI: 10.1007/s11032-016-0611-7