Breeding to increase beta-carotene levels in cereal grains, termed provitamin A biofortification, is an economical approach to address dietary vitamin A deficiency in the developing world. Experimental evidence from association and linkage populations in maize (Zea mays L.) demonstrate that the gene encoding beta-carotene hydroxylase 1 (crtRB1) underlies a principal quantitative trait locus associated with beta-carotene concentration and conversion in maize kernels. crtRB1 alleles associated with reduced transcript expression correlate with higher beta-carotene concentrations. Genetic variation at crtRB1 also affects hydroxylation efficiency among encoded allozymes, as observed by resultant carotenoid profiles in recombinant expression assays. The most favorable crtRB1 alleles, rare in frequency and unique to temperate germplasm, are being introgressed via inexpensive PCR marker-assisted selection into tropical maize germplasm adapted to developing countries, where it is most needed for human health.

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Multiple genomic regions explain variation in the carbon fixation response to non-stress and cold stress in Sorghum bicolor, with some of these regions simultaneously controlling multiple traits.

Leaf angle is defined as the inclination between the midrib of the leaf blade and the vertical stem of a plant. This trait has been identified as a key component in the development of high-yielding varieties of cereal species, particularly maize, rice, wheat, and sorghum. The effect of leaf angle on light interception efficiency, photosynthetic rate, and yield has been investigated since the 1960s, yet, significant knowledge gaps remain in understanding the genetic control of this complex trait. Recent advances in physiology and modeling have proposed a plant ideotype with varying leaf angles throughout the canopy. In this context, we present historical and recent evidence of: (i) the effect of leaf angle on photosynthetic efficiency and yield; (ii) the hormonal regulation of this trait; (iii) the current knowledge on its quantitative genetic control; and (iv) the opportunity to utilize high-throughput phenotyping methods to characterize leaf angle at multiple canopy levels. We focus on research conducted on grass species of economic importance, with similar plant architecture and growth patterns. Finally, we present the challenges and strategies plant breeders will need to embrace in order to manipulate leaf angle differentially throughout the canopy and develop superior crops for food, feed, and fuel production.

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Sorghum [Sorghum bicolor (L) Moench], an important grain and forage crop, is receiving significant attention as a lignocellulosic feedstock because of its water-use efficiency and high biomass yield potential. Because of the advancement of genotyping and sequencing technologies, genome-wide association study (GWAS) has become a routinely used method to investigate the genetic mechanisms underlying natural phenotypic variation. In this study, we performed a GWAS for nine grain and biomassrelated plant architecture traits to determine their overall genetic architecture and the specific association of allelic variants in gibberellin (GA) biosynthesis and signaling genes with these phenotypes. A total of 101 single-nucleotide polymorphism (SNP) representative regions were associated with at least one of the nine traits, and two of the significant markers correspond to GA candidate genes, GA2ox5 (Sb09 g028360) and KS3 (Sb06 g028210), affecting plant height and seed number, respectively. The resolution of a previously reported quantitative trait loci (QTL) for leaf angle on chromosome 7 was increased to a 1.67 Mb region containing seven candidate genes with good prospects for further investigation. This study provides new knowledge of the association of GA genes with plant architecture traits and the genomic regions controlling variation in leaf angle, stem circumference, internode number, tiller number, seed number, panicle exsertion, and panicle length. The GA gene affecting seed number variation (KS3, Sb06 g028210) and the genomic region on chromosome 7 associated with variation in leaf angle are also important outcomes of this study and represent the foundation of future validation studies needed to apply this knowledge in breeding programs. The increasing interest in biomass production for biofuel use is resulting in a paradigm shift in breeding for plant architecture parameters. The genetic manipulation of these traits can positively affect biomass production (Yuan et al., 2008) as suggested by the high correlations between biomass yield and plant height (Lubberstedt et al., 1997;Salas Fernandez et al., 2009) or leaf angle (Morinaka et al., 2006). Sorghum, the fifth most widely grown cereal crop in the world, is receiving significant attention as one of the most productive annual species for bioenergy production (Rooney et al., 2007) in addition to its well-known value as a grain and forage crop. Therefore, understanding the genetic control Core Ideas:• The 101 SNPs were associated with at least one of nine plant architecture traits• KS3 gene was associated with variation in seed number• GA2ox5 gene included in a significant region on chromosome 9 controlling plant height• Novel genomic regions were associated with stem circumference and internode number• Novel genomic regions were associated with tiller number, panicle exsertion, and length of plant architecture traits and applying that knowledge in sorghum breeding programs might be instrumental to develop improved germplasm for the incipient lignocell...

Patterns of linkage disequilibrium (LD) are of interest because they provide evidence of both equilibrium (e.g., mating system or long-term population structure) and nonequilibrium (e.g., demographic or selective) processes, as well as because of their importance in strategies for identifying the genetic basis of complex phenotypes. We report patterns of short and medium range (up to100 kb) LD in six unlinked genomic regions in the partially selfing domesticated grass, Sorghum bicolor. The extent of allelic associations in S. bicolor, as assessed by pairwise measures of LD, is higher than in maize but lower than in Arabidopsis, in qualitative agreement with expectations based on mating system. Quantitative analyses of the population recombination parameter, r, however, based on empirical estimates of rates of recombination, mutation, and self-pollination, show that LD is more extensive than expected under a neutral equilibrium model. The disparity between r and the population mutation parameter, u, is similar to that observed in other species whose population history appears to be complex. From a practical standpoint, these results suggest that S. bicolor is well suited for association studies using reasonable numbers of markers, since LD typically extends at least several kilobases but has largely decayed by 15 kb. T HE extent of allelic associations, commonly called linkage disequilibrium (LD), is of great interest in many species because of its implications for the design and feasibility of association studies and genome-wide scans to identify the genetic basis of complex traits. Genome-wide patterns of LD are fundamentally the product of two processes: (1) a new mutation occurs and is necessarily associated with the variants on the chromosome on which it arises, and (2) recombination places that mutation on a different genetic background, breaking the association. Thus the rate of recombination (r) is a key parameter in the process of LD decay. The relationship between r and LD is also affected by demographic factors. More specifically, the extent of LD is a reflection of the population recombination parameter, 4N e r, or r, where N e (effective population size) is a function of the long-term historical size of the population, population structure, and mating system. Similarly, the mutational process that generates associations is summarized in the population mutation parameter 4N e m, or u, where m is the mutation rate. At equilibrium in a randomly mating population without selection, the extent of allelic associations is simply a function of the relative rates of mutation and recombination, since 4N e cancels out in the ratio r/u. Nevertheless, even in this simplest of scenarios, LD decay varies widely in unlinked regions due to the substantial stochasticity of the evolutionary process (Nordborg and Tavare 2002).When a population departs from the panmictic equilibrium model, we can no longer accurately estimate r and u from empirical data, and observed levels of LD may be inconsistent with empirica...

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