Chloroplast DNA sequences are a primary source of data for plant molecular systematic studies. A few key papers have provided the molecular systematics community with universal primer pairs for noncoding regions that have dominated the field, namely trnL-trnF and trnK/matK. These two regions have provided adequate information to resolve species relationships in some taxa, but often provide little resolution at low taxonomic levels. To obtain better phylogenetic resolution, sequence data from these regions are often coupled with other sequence data. Choosing an appropriate cpDNA region for phylogenetic investigation is difficult because of the scarcity of information about the tempo of evolutionary rates among different noncoding cpDNA regions. The focus of this investigation was to determine whether there is any predictable rate heterogeneity among 21 noncoding cpDNA regions identified as phylogenetically useful at low levels. To test for rate heterogeneity among the different cpDNA regions, we used three species from each of 10 groups representing eight major phylogenetic lineages of phanerogams. The results of this study clearly show that a survey using as few as three representative taxa can be predictive of the amount of phylogenetic information offered by a cpDNA region and that rate heterogeneity exists among noncoding cpDNA regions.

The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis

Legumes, broadly defined by their unusual flower structure, podded fruit, and the ability of 88% of the species examined to date to form nodules with rhizobia ([de Faria et al., 1989][1]), are second only to the Graminiae in their importance to humans. The 670 to 750 genera and 18,000 to 19,000

Legumes: Importance and Constraints to Greater Use

We report a large-scale analysis of the patterns of genome-wide genetic variation in soybeans. We re-sequenced a total of 17 wild and 14 cultivated soybean genomes to an average of approximately ×5 depth and >90% coverage using the Illumina Genome Analyzer II platform. We compared the patterns of genetic variation between wild and cultivated soybeans and identified higher allelic diversity in wild soybeans. We identified a high level of linkage disequilibrium in the soybean genome, suggesting that marker-assisted breeding of soybean will be less challenging than map-based cloning. We report linkage disequilibrium block location and distribution, and we identified a set of 205,614 tag SNPs that may be useful for QTL mapping and association studies. The data here provide a valuable resource for the analysis of wild soybeans and to facilitate future breeding and quantitative trait analysis.

Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection

The use of crop wild relatives (CWR) genes to improve crop performance is well established with important examples dating back more than 60 years. In this paper, we review available information on the presence of genes from CWR in released cultivars of 16 mandate crops of the CGIAR institutes, and some selected additional crops, focusing on the past 20 years—the period since a comprehensive review by Robert and Christine Prescott-Allen in 1986. It appears that there has been a steady increase in the rate of release of cultivars containing genes from CWR. While there continues to be a strong emphasis on using pest and disease resistance genes, a wider range of characteristics are being introduced than in the past. Those crops whose wild relatives have traditionally been used as sources of useful traits (e.g., wheat, tomato) continue to be most likely to include new genes from their wild relatives. CWR are continually gaining in importance and prevalence, but, we argue, their contributions to the development of new cultivars remain less than might have been expected given improved procedures for intercrossing species from different gene pools, advances in molecular methods for managing backcrossing programes, increased numbers of wild species accessions in gene banks, and the substantial literature on beneficial traits associated with wild relatives.

The use of wild relatives in crop improvement: a survey of developments over the last 20 years

There are a number of components present in soybeans that exert a negative impact on the nutritional quality of the protein. Among those factors that are destroyed by heat treatment are the protease inhibitors and lectins. Protease inhibitors exert their antinutritional effect by causing pancreatic hypertrophy/hyperplasia, which ultimately results in an inhibition of growth. The lectin, by virtue of its ability to bind to glycoprotein receptors on the epithelial cells lining the intestinal mucosa, inhibits growth by interfering with the absorption of nutrients. Of lesser significance are the antinutritional effects produced by relatively heat stable factors, such as goitrogens, tannins, phytoestrogens, flatus-producing oligosaccharides, phytate, and saponins. Other diverse but ill-defined factors appear to increase the requirements for vitamins A, B12, D, and E. The processing of soybeans under severe alkaline conditions leads to the formation of lysinoalanine, which has been shown to damage the kidneys of rats. This is not generally true, however, for edible soy protein that has been produced under milder alkaline conditions. Also meriting consideration is the allergenic response that may sometimes occur in humans, as well as calves and piglets, on dietary exposure to soybeans.

Implications of antinutritional components in soybean foods

Soybeans, together with bananas, barley, common beans, cassavas, coconuts, maize, peanuts, potatoes, rice, sorghum, sugar beets, sugarcane, sweet potatoes and wheat, are man's principal food plants (12). Today, the soybean, like so many other food plants, is taken for granted, that is, without appreciable forethought as to when and where it was adapted to the needs of man, how, when and by whom it was disseminated, and whether or not the distribution of soybeans took place in prehistoric or within the modern era (73). In addition to the general lack of urgency in studying the origin of the soybean, it is unfortunate that the literature concerned with the antiquity and historical development of the soybean and its agricultural consequences is fraught with errors and misconceptions. This is mainly due to two reasons: (a) the soybean is autochthonous to the Orient, where western scientists are at a linguistic disadvantage with respect to historical records; (b) it is only in recent times that attention has been focused on studying in depth, using a team approach, the interrelationships between the domestication of plants and animals and development and needs of human society (10, 32, 67, 115). During the past 30 years, many Chinese historical books, commentaries and material media have been translated into western languages and a large amount of archeological material has been uncovered, both on mainland China and in Taiwan. This paper is an attempt to reconcile the old archeological, historical, agricultural and botanical literature with the more recent data and to establish a working hypothesis on the domestication of the soybean.

On the domestication of the soybean

Seed protein electrophoresis is increasingly being utilized as an additional approach for species identification and as a useful tool for tracing back the evolution of various groups of plants. This paper summarizes the main features of the seed protein profile — stability, uniformity and additive nature. In addition, the significance of this approach for resolving specific taxonomic and evolutionary problems is pointed out.

Seed protein electrophoresis in taxonomic and evolutionary studies.

The genusGlycine has had a stormy taxonomic history. Recent studies of herbarium specimens and cytological and morphological analyses of living collections, coupled with chemotaxonomic investigations, have made it necessary to revise the genus. In the first part of this paper the current taxonomic status of the genusGlycine is reviewed. The soybean was domesticated in China. It is unfortunate that the literature concerned with the antiquity and historical development of the soybean is obscured by legends and myths. In the second section of the paper, the archeological, historical, agricultural and botanical literature is summarized in order to present all the known evidence as to when, where and by whom the soybean was domesticated. The soybean is the world’s premier source of dietary vegetable oil and is nutritionally an excellent and inexpensive source of protein for use either as human food or animal feed. In addition, the soybean has numerous industrial uses. In the last section of this paper the traditional uses of fermented and nonfermented soybeans in the East as well as the high-technology-developed uses of soybeans in the West are summarized.

Taxonomy of the genus Glycine , domestication and uses of soybeans

This study was conducted with the objective of determining the genomic relationship between cultivated soybean (Glycine max) and wild soybean (G. soja) of the subgenus Soja, genus Glycine. Observations on cross-ability rate, hybrid viability, meiotic chromosome pairing, and pollen fertility in F
1 hybrids of G. max × G. soja and reciprocals elucidated that both species hybridized readily and set mature putative hybrid pods, generated vigorous F1 plants, had a majority of sporocytes that showed 18II + 1IV chromosome association at diakinesis and metaphase I, and had a pollen fertility that ranged from 49.2% to 53.3%. A quadrivalent was often associated with the nucleolus, suggesting that one of the chromosomes involved in the interchange is a satellited chromosome. Thus, G. max and G. soja genetic stocks used in this study have been differentiated by a reciprocal translocation. Pachytene analysis of F1 hybrids helped construct chromosome maps based on chromosome length and euchromatin and heterochromatin distribution. Chromosomes were numbered in descending order of 1–20. Pachytene chromosomes in soybean showed heterochromatin distribution on either side of the centromeres. Pachytene analysis revealed small structural differences for chromosomes 6 and 11 which were not detected at diakinesis and metaphase I. This study suggests that G. max and G. soja carry similar genomes and validates the previously assigned genome symbol GG.

Theodore Hymowitz

Papers

On the domestication of the soybean

Seed protein electrophoresis in taxonomic and evolutionary studies.

Taxonomy of the genus Glycine , domestication and uses of soybeans

The genomic relationship between Glycine max (L.) Merr. and G. soja Sieb. and Zucc. as revealed by pachytene chromosome analysis.

Speciation and Cytogenetics