Soybean improvement via plant breeding has been critical for the success of the crop. The objective of this study was to quantify genetic change in yield and other traits that occurred during the past 80 yr of North American soybean breeding in Maturity Groups (MGs) II, III, and IV. Historic sets of 60 MG II, 59 MG III, and 49 MG IV soybean cultivars, released from 1923 to 2008, were evaluated in field trials conducted in 17 U.S. states and one Canadian province during 2010 to 2011. Averaged over 27 MG II and MG IV and 26 MG III site-years of data, the estimated rates of yield improvement during the 80 yr were 23 kg ha -1 yr -1 for MGs II and III, and 20 kg ha -1 yr -1 for MG IV cultivars. However, a two-segment linear regression model provided a better fit to the data and indicated that the average current rate of genetic yield gain across MGs is 29 kg ha -1 yr -1 . Modern cultivars yielded more than old cultivars in all environments, but particularly in high-yielding environments. New cultivars in the historic sets used in this study are shorter in height, mature later, lodge less, and have seeds with less protein and greater oil concentration. Given that on-farm soybean yields in the United States are also increasing at a rate of 29 kg ha -1 yr -1 , it can be inferred that continual release of greater-yielding cultivars has been a substantive driver of the U.S. onfarm realized yield increases.

Soybean is the world’s leading source of vegetable protein and demand for its seed continues to grow. Breeders have successfully increased soybean yield, but the genetic architecture of yield and key agronomic traits is poorly understood. We developed a 40-mating soybean nested association mapping (NAM) population of 5,600 inbred lines that were characterized by single nucleotide polymorphism (SNP) markers and six agronomic traits in field trials in 22 environments. Analysis of the yield, agronomic, and SNP data revealed 23 significant marker-trait associations for yield, 19 for maturity, 15 for plant height, 17 for plant lodging, and 29 for seed mass. A higher frequency of estimated positive yield alleles was evident from elite founder parents than from exotic founders, although unique desirable alleles from the exotic group were identified, demonstrating the value of expanding the genetic base of US soybean breeding.

A new, widespread disease was recently observed in soybean in the United States. The disease, named Soybean vein necrosis, is manifested by intraveinal chlorosis and necrosis, and has been found in almost all of the 50 fields visited over a period of 3 years in the midwest and midsouth part of the United States. A virus was isolated from symptomatic material, and detection protocols were developed. More than 150 symptomatic specimens collected from seven US States were tested, and all were found positive for the virus unlike 75 asymptomatic samples, revealing the absolute association between virus and disease. Protein pairwise comparisons coupled with phylogenetic analyses indicate that the virus is a new member of the genus Tospovirus.

Advances in the use of diploid Asiatic species in cotton breeding require an understanding of the relatedness and ancestry of diploid cotton accessions, and identification of simple sequence repeat (SSR) markers associated with agronomically important phenotypic traits, for example, fibre quality. Fifty-six Gossypium arboreum germplasm accessions introduced from nine regions of Africa, Asia and Europe were evaluated for eight fibre characters (lint percentage, lint colour, elongation, micronaire, strength, 50% span length, 2.5% span length and maturity%) and genotyped with 98 SSR markers. When viewed across all accessions most of the SSR markers were polymorphic. Population structure analysis identified six main clusters for the accessions which corresponded to different geographic regions, indicating agreement between genetic and predefined populations. The general linear model method was used to disclose marker-trait associations. Marker-trait associations were investigated by fitting single marker regression models for phenotypic traits on marker band intensities with correction for population structure. This paper illustrates the potential of association mapping in diploid cotton, because existing phenotypic data, a modest number of SSR markers, and a pioneering statistical analysis, identified interesting associations.

This study reports a high density genetic linkage map based on the ‘Maryland 96-5722’ by ‘Spencer’ recombinant inbred line (RIL) population of soybean [Glycine max (L.) Merr.] and constructed exclusively with single nucleotide polymorphism (SNP) markers. The Illumina Infinium SoySNP6K BeadChip genotyping array produced 5,376 SNPs in the mapping population, with a 96.75% success rate. Significant level of goodness-of-fit for each locus was tested based on the observed vs. expected ratio (1:1). Out of 5,376 markers, 1,465 SNPs fit the 1:1 segregation rate having ≤20% missing data plus heterozygosity among the RILs. Among this 1,456 just 657 were polymorphic between the parents DNAs tested. These 657 SNPs were mapped using the JoinMap 4.0 software and 550 SNPs were distributed on 16 linkage groups (LGs) among the 20 chromosomes of the soybean genome. The total map length was just 201.57 centiMorgans (cM) with an average marker density of 0.37 cM. This is one of the high density SNP-based genetic linkage maps of soybean that will be used by the scientific community to map quantitative trait loci (QTL) and identify candidate genes for important agronomic traits in soybean.

The cultivated diploid, Gossypium arboreum L., (A genome) is an invaluable genetic resource for improving modern tetraploid cotton (G. hirsutum L. and G. barbadense L.) cultivars. The objective of this research is to select a set of informative and robust microsatellites for studying genetic relationships among accessions of geographically diverse G. arboreum cultivars. From more than 1,500 previously developed simple sequence repeat (SSR) markers, 115 genomic (BNL) and EST-derived (MUCS and MUSS) markers were used to evaluate the allelic diversity of a core panel of G. arboreum accessions. These SSR data enabled advanced genome analyses. A set of 25 SSRs were selected based both upon their high level of informativeness (PIC > or = 0.50) and the production of clear PCR bands on agarose gels. Subsequently, 96 accessions representing a wide spectrum of diversity of G. arboreum cultivars were analyzed with these markers. The 25 SSR loci revealed 75 allelic variants (polymorphisms) ranging from 2 to 4 alleles per locus. The Neighborjoining (NJ) method, based on genetic dissimilarities, revealed that cultivars from geographically adjacent countries tend to cluster together. Outcomes of this research should be useful in decreasing redundancy of effort and in constructing a core collection of G. arboreum, important for efficient use of this genetic resource in cotton breeding.

LG-E (Chr_15), LG-J (Chr_16), and LG-G (Chr_18). The SNP markers closely linked to the QTL reported here will be useful for development of cultivars with altered oil and fatty acid compositions in soybean breeding programs.

Crop productivity is severely reduced by water deficit and drought in many plant species including soybean. Improved root and shoot traits can contribute to drought tolerance ability of the plant. This research was conducted to identify QTL that underlie several root and shoot traits in the ‘Essex’ by ‘Forrest’ (ExF RILs, n=94) recombinant inbred line (RIL) soybean population. Field collected samples were used for gathering phenotypic data of basal root thickness (BRT), lateral root number (LRN), maximum root length (MRL), root fresh weight (RFW), root dry weight (RDW), shoot fresh weight (SFW), shoot dry weight (SDW), and calculating RFW/SFW, and RDW/SDW ratios. All traits and ratios were compared against DNA markers using the composite interval mapping (CIM). A total of 12 QTL: 3 for MRL, 1 QTL for LRN, 1 QTL for BRT, 2 QTL for RFW, 2 QTL for RDW, 4 QTL for SFW, 3 QTL for SDW, and 3 QTL for SFW/SDW were identified and mapped on different linkage groups (LGs) A2, B2, C2, D1a, F, G, and N. The LOD scores of these QTL ranged from 2.5 to 6.0. No QTL were associated with RFW/RDW. The root and shoot trait QTL of this study may benefit breeding programs for producing cultivars tolerant to water deficit and high yield. Preliminary analyses of genes the QTL regions using GO annotation gave insight into genes that may underlie some of these QTLs.