Wheat (Triticum aestivum L.) grain quality traits that are controlled by quantitative traits loci (QTL) define suitable growing areas and potential end-use products of a wheat cultivar. To dissect QTL for these traits including protein content (GPC); test weight (TW); single kernel characterization system (SKCS)-estimated kernel weight (SKW); kernel diameter (KD); kernel hardness measured by near-infrared reflectance spectroscopy (NIRS) hardness index (NHI); and SKCS-hardness index (SHI), a high-density genetic map with single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers was developed using recombinant inbred lines (RILs) derived from Ning7840 ¡Á Clark. The RILs were evaluated for these quality traits in seven Oklahoma environments from 2001 to 2003. A total of 41 QTL with additive effects on different traits were mapped on most wheat chromosomes, excluding 1A, 2A, 3D, 4D, 6D, and 7B. Seven chromosome regions showed either tightly linked QTL or QTL with pleiotropic effects on two to four traits. Ten pairs of QTL showed additive ¡Á additive effects (AA), four QTL were involved in additive ¡Á environment (AE) effects, and one was involved in AAE effects. Two to eleven QTL for each of the six traits and 139 tightly linked markers to these QTL were identified. The findings shed light on the inheritance of wheat grain quality traits and provide DNA markers for manipulating these important traits to improve quality of new wheat cultivars.

To enhance the yield potential of an elite indica rice cultivar, an introgression (BC₃-derived) line of IR64, YTH288, was developed using a new-plant-type cultivar, IR66215-44-2-3, as a donor parent. YTH288 has agronomically valuable characteristics such as large panicles, few unproductive tillers, and large leaves inherited from NPT. To identify the genetic basis of these traits, we used 167 F₂ plants derived from a cross between IR64 and YTH288 to conduct QTL analysis for five agronomic traits: days to heading (DTH), culm length (CL), flag leaf length (FLL), flag leaf width (FLW), and filled spikelet number per panicle (FSN). Six putative QTL were detected: four on chromosome 4 (for CL, FLL, FLW, and FSN) and two on chromosome 2 (for DTH and FLL). All QTL with the IR66215-44-2-3 allele, except that for FLL on chromosome 2, had positive effects on each trait. To confirm the effects of these putative QTL, we developed NILs with the IR64 genetic background by marker-assisted selection. We observed significant differences in several agronomic traits between IR64 and NILs that carried these QTL on chromosomes 2 and 4. Additionally, four IR64-NILs carrying chromosomal segments derived from different NPT varieties on the long arm of chromosome 4 exhibited similar pleiotropic effects for unique agronomic traits. These NILs can be used as research materials for studying each trait and as breeding materials for yield improvement of indica rice cultivars.

Many complex traits are highly correlated rather than independent. By taking the correlation structure of multiple traits into account, joint association analyses can achieve both higher statistical power and more accurate estimation. To develop a statistical approach to joint association analysis that includes allele detection and genetic effect estimation, we combined multivariate partial least squares regression with variable selection strategies and selected the optimal model using the Bayesian Information Criterion (BIC). We then performed extensive simulations under varying heritabilities and sample sizes to compare the performance achieved using our method with those obtained by single-trait multilocus methods. Joint association analysis has measurable advantages over single-trait methods, as it exhibits superior gene detection power, especially for pleiotropic genes. Sample size, heritability, polymorphic information content (PIC), and magnitude of gene effects influence the statistical power, accuracy and precision of effect estimation by the joint association analysis.

Seed aging decreases the quality and vigor of crop seeds, thereby causing substantial agricultural and economic losses in crops. To identify genetic differences in seed aging between homozygotes and heterozygotes in maize, the seeds of a set of recombinant inbred lines (RILs) and an immortalized F₂ (IF₂) population were subjected to artificial aging treatments for 0, 2, 3, and 4 days under 45 ºC and 85% relative humidity and seed vigor was then evaluated in a field experiment. Seed vigor of all entries tested decreased sharply with longer aging treatment and seed vigor decreased more slowly in heterozygotes than in homozygotes. Forty-nine QTL were detected for four measured seed vigor traits in the RIL (28 QTL) and IF₂ (21 QTL) populations. Only one QTL, qGP5, was detected in both populations, indicating that the genes involved in anti-aging mechanisms differed between inbred lines and hybrids. Several QTL were identified to be responsible for multiple seed vigor traits simultaneously in the RIL and IF₂ populations under artificial aging conditions. These QTL may include major genes for seed vigor or seed aging. QTL qVI4b and qGE3a detected in the RIL population coincided with genes ZmLOX1 and ZmPLD1 in the same respective chromosomal regions. These QTL would be useful for screening for anti-aging genes in maize breeding.

Rice bean (Vigna umbellata Thunb.), a warm-season annual legume, is grown in Asia mainly for dried grain or fodder and plays an important role in human and animal nutrition because the grains are rich in protein and some essential fatty acids and minerals. With the aim of expediting the genetic improvement of rice bean, we initiated a project to develop genomic resources and tools for molecular breeding in this little-known but important crop. Here we report the construction of an SSR-enriched genomic library from DNA extracted from pooled young leaf tissues of 22 rice bean genotypes and developing SSR markers. In 433,562 reads generated by a Roche 454 GS-FLX sequencer, we identified 261,458 SSRs, of which 48.8% were of compound form. Dinucleotide repeats were predominant with an absolute proportion of 81.6%, followed by trinucleotides (17.8%). Other types together accounted for 0.6%. The motif AC/GT accounted for 77.7% of the total, followed by AAG/CTT (14.3%), and all others accounted for 12.0%. Among the flanking sequences, 2928 matched putative genes or gene models in the protein database of Arabidopsis thaliana, corresponding with 608 non-redundant Gene Ontology terms. Of these sequences, 11.2% were involved in cellular components, 24.2% were involved molecular functions, and 64.6% were associated with biological processes. Based on homolog analysis, 1595 flanking sequences were similar to mung bean and 500 to common bean genomic sequences. Comparative mapping was conducted using 350 sequences homologous to both mung bean and common bean sequences. Finally, a set of primer pairs were designed, and a validation test showed that 58 of 220 new primers can be used in rice bean and 53 can be transferred to mung bean. However, only 11 were polymorphic when tested on 32 rice bean varieties. We propose that this study lays the groundwork for developing novel SSR markers and will enhance the mapping of qualitative and quantitative traits and marker-assisted selection in rice bean and other Vigna species.

Crop biofortification is a sustainable approach for fighting micronutrient malnutrition in the world. The estimation of variance components in genetically broad-based populations provides information about their genetic architecture, allowing the design of an appropriate biofortification breeding method for cross-pollinated crops such as pearl millet. The objective of this study was to estimate intra-population genetic variance using self (S₁) and half-sib (HS) progenies in two populations, AIMP92901 and ICMR312. Field trials were evaluated in two contrasting seasons (2009 rainy and 2010 summer; otherwise called environments) in Alfisols at ICRISAT, Patancheru. Analyses of variance showed highly significant variation for S₁s and HS progenies, reflecting high within-population genetic variation for both micronutrients and other key traits. However, the HS showed narrow ranges and lower genetic variances than the S₁ for all of the traits. The micronutrients were highly positively correlated in S₁ (r = 0.77 to 0.86; P < 0.01) and HS (r = 0.74 to 0.77; P < 0.01) progenies of both populations, implying concurrent genetic improvement for both micronutrients. The genetic variance component was different among populations for Fe and Zn contents across environments, with AIMP92901 showing a greater proportion of dominance and ICMR312 greater additive variance for these micronutrients. The estimates of variance (additive and dominance) were specific for each population, given their dependence on the additive and dominance effects of the segregating loci, which also differ among populations. The possible causes for such differences were discussed. The results showed that the expression of these micronutrients in pearl millet shows largely additive variance, so that breeding high-iron hybrids will require incorporation of these micronutrient traits into both parental lines.

The maize mutant gene Vestigial glume 1 (Vg1) has been fine-mapped to a narrow region by map-based cloning and the candidate gene for Vg1 spanned 19.5 kb. Here we report Vg1 genomic fosmid library construction and screening. The fosmid library of Vg1 consisted of 574,000 clones with an average insert size of 36.4 kb, representing 7.9-fold coverage of the maize genome. Fosmid stability assays indicated that clones were stable during propagation in the fosmid system. Using Vg1 candidate gene-specific primers, a positive clone was successfully identified. This discovery will pave the way for identifying the function of Vg1 in maize development.

Sorghum is an important staple food crop of Asian and African countries. As a “poor man's crop”, it provides dietary starch, protein, and some vitamins and minerals. Minerals are important for various physiological functions in the human body. As a major staple crop of central and southern Indian provinces, sorghum landraces are a source of supplementary micronutrients. Concentrations of micronutrients and protein and yield parameters were studied using 112 local landraces and varieties. Univariate analysis revealed wide variation for iron (1.10-9.54 mg 100 g^{− 1}), zinc (1.12-7.58 mg 100 g^{− 1}), protein (3.50-12.60%), and grain yield (2.50-76.50 g) among the landraces. High estimates of genetic/phenotypic coefficient of variation, and genetic advances over the mean were identified for landraces and varieties. High heritabilities were also identified for yield and mineral content. Correlation estimates among the genotypes indicated that grain yield was positively correlated with copper and protein with copper and zinc. Cluster analysis based on Euclidean distance resolved all of the genotypes into three major clusters. The wide range of values with high heritability estimates may favor the use of these landraces in recombination breeding to improve nutritional quality in sorghum.

The objective of this study was to characterize the phaseolin type and α-amylase (αAI) level in common bean (Phaseolus vulgaris L.) accessions deposited in the Chinese National Genebank. The 40 accessions sampled were common varieties originating in Asia, North America, South America, Europe, and Africa. No Inca (I-) phaseolin was observed in the accessions. Only four accessions contained Tendergreen (T-) phaseolin and the remaining 36 contained Sanilac (S-) phaseolin. αAI proteins extracted from nine accessions showed higher α-amylase inhibitory activity than the control (Phase 2, IC₅₀ = 0.65 μg). These common bean accessions have potential use as nutraceutical ingredients.