Differential SW16.1 allelic effects and genetic backgrounds contributed to increased seed weight after soybean domestication.

Although seed weight has increased following domestication from wild soybean (Glycine soja) to cultivated soybean (Glycine max), the genetic basis underlying this change is unclear. Using mapping populations derived from chromosome segment substitution lines of wild soybean, we identified SW16.1 as the causative gene underlying a major quantitative trait locus controlling seed weight. SW16.1 encodes a nucleus-localized LIM domain-containing protein. Importantly, the GsSW16.1 allele from wild soybean accession N24852 had a negative effect on seed weight, whereas the GmSW16.1 allele from cultivar NN1138-2 had a positive effect. Gene expression network analysis, reverse-transcription quantitative polymerase chain reaction, and promoter-luciferase reporter transient expression assays suggested that SW16.1 regulates the transcription of MT4, a positive regulator of seed weight. The natural variations in SW16.1 and other known seed weight genes were analyzed in soybean germplasm. The SW16.1 polymorphism was associated with seed weight in 247 soybean accessions, showing much higher frequency of positive-effect alleles in cultivated soybean than in wild soybean. Interestingly, gene allele matrix analysis of the known seed weight genes revealed that G. max has lost 38.5% of the G. soja alleles and that most of the lost alleles had negative effects on seed weight. Our results suggest that eliminating negative alleles from G. soja led to a higher frequency of positive alleles and changed genetic backgrounds in G. max, which contributed to larger seeds in cultivated soybean after domestication from wild soybean. Our findings provide new insights regarding soybean domestication and should assist current soybean breeding programs.

Germplasm Sources, Genetic Richness, and Population Differentiation of Modern Chinese Soybean Cultivars Based on Pedigree Integrated With Genomic-Marker Analysis.

Soybean is a native crop in China for ≈ 5,000 years. The 560 cultivars released in 2006-2015, commercialized with seeds available publicly, were collected (designated modern Chinese soybean cultivars, MCSCs), as a part of 2,371 ones released during ~100 years' breeding history. The MCSCs with their parental pedigrees were gathered, including 279, 155, and 126 cultivars from Northeast and Northwest China (NNC), Huang-Huai-Hai Valleys (HHH), and Southern China (SC), respectively. The MCSCs were tested in the field, genotyped with sequencing, and analyzed for their germplasm sources, genetic richness, and population differentiation based on pedigree integrated with genomic-marker analysis. The main results were as follows: (i) The MCSCs covering 12 of the global 13 MGs (maturity groups) showing different ecoregions with different cropping systems caused their different MG constitutions. (ii) Parental pedigree analysis showed 718 immediate parents and 604 terminal ancestors involved in MCSCs, from which 41 core-terminal ancestors were identified. (iii) NNC was richer in allele number and specific present/deficient alleles, and genetically distant from HHH and SC. (iv) The geographic grouping of MCSCs was partially consistent with marker-based clustering, indicating multiple genetic backgrounds in three eco-subpopulations. (v) Eleven major core-terminal ancestor-derived families were identified, including four derived from ancestors in NNC, four from HHH, and three from SC, containing 463 (82.68%) MCSCs with some cross-distribution among ecoregions. (vi) CGS (coefficient of genetic similarity) calculated from genomic markers showed more precision than COP (coefficient of parentage) using pedigree information in evaluating genetic relationship/differentiation. Overall, through pedigree and genomic-marker analyses, the germplasm constitutions of the three eco-subpopulations were relatively self-sufficient, and germplasm exchange is seriously required for further improvement.

Identification of the QTL-allele System Underlying Two High-Throughput Physiological Traits in the Chinese Soybean Germplasm Population.

The QTL-allele system underlying two spectral reflectance physiological traits, NDVI (normalized difference vegetation index) and CHL (chlorophyll index), related to plant growth and yield was studied in the Chinese soybean germplasm population (CSGP), which consisted of 341 wild accessions (WA), farmer landraces (LR), and released cultivars (RC). Samples were evaluated in the Photosynthetic System II imaging platform at Nanjing Agricultural University. The NDVI and CHL data were obtained from hyperspectral reflectance images in a randomized incomplete block design experiment with two replicates. The NDVI and CHL ranged from 0.05-0.18 and 1.20-4.78, had averages of 0.11 and 3.57, and had heritabilities of 78.3% and 69.2%, respectively; the values of NDVI and CHL were both significantly higher in LR and RC than in WA. Using the RTM-GWAS (restricted two-stage multi-locus genome-wide association study) method, 38 and 32 QTLs with 89 and 82 alleles and 2-4 and 2-6 alleles per locus were identified for NDVI and CHL, respectively, which explained 48.36% and 51.35% of the phenotypic variation for NDVI and CHL, respectively. The QTL-allele matrices were established and separated into WA, LR, and RC submatrices. From WA to LR + RC, 4 alleles and 2 new loci emerged, and 1 allele was excluded for NDVI, whereas 6 alleles emerged, and no alleles were excluded, in LR + RC for CHL. Recombination was the major motivation of evolutionary differences. For NDVI and CHL, 39 and 32 candidate genes were annotated and assigned to GO groups, respectively, indicating a complex gene network. The NDVI and CHL were upstream traits that were relatively conservative in their genetic changes compared with those of downstream agronomic traits. High-throughput phenotyping integrated with RTM-GWAS provides an efficient procedure for studying the population genetics of traits.

Evolutionary QTL-allele changes in main stem node number among geographic and seasonal subpopulations of Chinese cultivated soybeans.

The main stem node number (MSN) is a trait related to geographic adaptation, plant architecture and yield potential of soybean. The QTL-allele constitution of the Chinese Cultivated Soybean Population (CCSP) was identified using the RTM-GWAS (restricted two-stage multi-locus genome-wide association study) procedure, from which a QTL-allele matrix was established and then separated into submatrices to explore the genetic structure, evolutionary differentiation, breeding potential and candidate genes of MSN in CCSP. The MSN of 821 accessions varied from 8.8 to 31.1, with an average of 16.3 in Nanjing, China (32.07° N, 118.62° E), where the MSNs of all the materials could be evaluated in a standardized manner. Among the six geo-seasonal subpopulations, the MSN varied from 21.7 in a southern summer-autumn-sowing subpopulation (SA-IV) down to 13.5 in a northeastern spring-sowing subpopulation (SP-I). The materials were genotyped with restriction site-associated DNA-sequencing. Totally 142 main-effect QTLs (73.24% new) with 560 alleles contributing 72.98% to the phenotypic variance were identified. The evolutionary QTL-allele changes in MSN from SA-IV through SP-I showed that inheritance (78.93% of alleles) was the primary factor influencing the evolution of this trait, followed by allele emergence (19.64% alleles), allele exclusion (1.43% alleles), and recombination among retained alleles. In the evolutionary changes, 70 QTLs, including 12 newly emerged QTLs, with 118 alleles were involved. An increase potential of 2-8 nodes was predicted and 112 candidate genes were annotated and preliminarily verified with χ2-tests in the CCSP. The RTM-GWAS showed powerful in detecting QTL-allele system, assessing evolution factors, predicting optimal crosses and identifying candidate genes in a germplasm population.

Bi-Phenotypic Trait May Be Conferred by Multiple Alleles in a Germplasm Population.

The Chinese soybean germplasm pool (CSGP) comprises annual wild (WA), farmers' landrace (LR) and released cultivar (RC) populations, and ecoregion subpopulations in WA/LR/RC (ecoregion IV/III/II/I). A representative sample consisted of 1,024 accessions was studied for pubescence color (PC) and flower color (FC). In the evolution from WA (brown PC and mainly purple FC) to LR then to RC, with above wild characteristic changed, while gray PC, and white FC emerged and their frequency increased. Using 36,952 genomic SNPLDB markers with 100,092 haplotypes, the association between markers and bi-phenotypic traits was detected using χ2 association analysis under single locus model and RTM-GWAS procedure under multi-locus model, respectively. Multiple markers co-associated with individual bi-phenotypic trait with the most significant markers containing multiple rather than two haplotypes even for a bi-phenotypic trait. On a marker/locus, each haplotype corresponds to two colors, except one (FC-1-5) out of 11 haplotypes for single color. The major candidate gene was annotated with its alleles identified from the population sequencing data. Similarly, multiple alleles identified and each corresponds to two colors except three (a8/a9/b3) out of 12 alleles for single color. The major haplotypes/alleles in LR and RC were traced to WA ecoregion subpopulations, the WA IV and WA III genotypes showed genetically more close to the cultivated subpopulations, therefore, WA from Ecoregion IV and III were inferred as the common ancestor for cultivated soybeans. The marker-haplotypes/gene-alleles not exactly coincided with the bi-phenotypic trait has challenged to the traditional Mendelian genetics, which was discussed and to be further studied.