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Bin Han and colleagues present a genome-wide association analysis of grain size and shape in cultivated rice and identify a major locus for grain size encoding the transcription factor OsSPL13. They find that the large-grain allele in tropical japonica cultivars was introgressed from indica varieties during selection for improved grain yield. Although genetic diversity has a cardinal role in domestication, abundant natural allelic variations across the rice genome that cause agronomically important differences between diverse varieties have not been fully explored. Here we implement an approach integrating genome-wide association testing with functional analysis on grain size in a diverse rice population. We report that a major quantitative trait locus, GLW7 , encoding the plant-specific transcription factor OsSPL13, positively regulates cell size in the grain hull, resulting in enhanced rice grain length and yield. We determine that a tandem-repeat sequence in the 5′ UTR of OsSPL13 alters its expression by affecting transcription and translation and that high expression of OsSPL13 is associated with large grains in tropical japonica rice. Further analysis indicates that the large-grain allele of GLW7 in tropical japonica rice was introgressed from indica varieties under artificial selection. Our study demonstrates that new genes can be effectively identified on the basis of genome-wide association data.

Individual grain weight is a major yield component in wheat. To provide a comprehensive understanding of grain weight determination, the carpel size at anthesis, grain dry matter accumulation, grain water uptake and loss, grain morphological expansion, and final grain weight at different positions within spikelets were investigated in a recombinant inbred line mapping population of bread wheat (Triticum aestivum L.)×spelt (Triticum spelta L.). Carpel size, grain dry matter and water accumulation, and grain dimensions interacted strongly with each other. Furthermore, larger carpels, a faster grain filling rate, earlier and longer grain filling, more grain water, faster grain water absorption and loss rates, and larger grain dimensions were associated with higher grain weight. Frequent quantitative trait locus (QTL) coincidences between these traits were observed, particularly those on chromosomes 2A, 3B, 4A, 5A, 5DL, and 7B, each of which harboured 16−49 QTLs associated with >12 traits. Analysis of the allelic effects of coincident QTLs confirmed their physiological relationships, indicating that the complex but orderly grain filling processes result mainly from pleiotropy or the tight linkages of functionally related genes. After grain filling, distal grains within spikelets were smaller than basal grains, primarily due to later grain filling and a slower initial grain filling rate, followed by synchronous maturation among different grains. Distal grain weight was improved by increased assimilate availability from anthesis. These findings provide deeper insight into grain weight determination in wheat, and the high level of QTL coincidences allows simultaneous improvement of multiple grain filling traits in breeding.

Identification of grain shape determining genes can facilitate breeding of rice cultivars with optimal grain shape and appearance quality. Here, we identify GS9 ( Grain Shape Gene on Chromosome 9 ) gene by map-based cloning. The gs9 null mutant has slender grains, while overexpression GS9 results in round grains. GS9 encodes a protein without known conserved functional domain. It regulates grain shape by altering cell division. The interaction of GS9 and ovate family proteins OsOFP14 and OsOFP8 is modulated by OsGSK2 kinase, a key regulator of the brassinosteroids signaling pathway. Genetic interaction analysis reveals that GS9 functions independently from other previously identified grain size genes. Introducing the gs9 allele into elite rice cultivars significantly improves grain shape and appearance quality. It suggests potential application of gs9 , alone or in combination with other grain size determining genes, in breeding of rice varieties with optimized grain shape. Rice grain shape or size is an important trait associated with both yield and appearance quality. Here, the authors identify GS9 as a negative transcription regulator of slender grain and show it can improve grain shape and appearance independently from other previously identified grain size genes.

Dissecting the genetic basis of complex traits is aided by frequent and nondestructive measurements. Advances in range imaging technologies enable the rapid acquisition of three-dimensional (3D) data from an imaged scene. A depth camera was used to acquire images of sorghum (Sorghum bicolor), an important grain, forage, and bioenergy crop, at multiple developmental time points from a greenhouse-grown recombinant inbred line population. A semiautomated software pipeline was developed and used to generate segmented, 3D plant reconstructions from the images. Automated measurements made from 3D plant reconstructions identified quantitative trait loci for standard measures of shoot architecture, such as shoot height, leaf angle, and leaf length, and for novel composite traits, such as shoot compactness. The phenotypic variability associated with some of the quantitative trait loci displayed differences in temporal prevalence; for example, alleles closely linked with the sorghum Dwarf3 gene, an auxin transporter and pleiotropic regulator of both leaf inclination angle and shoot height, influence leaf angle prior to an effect on shoot height. Furthermore, variability in composite phenotypes that measure overall shoot architecture, such as shoot compactness, is regulated by loci underlying component phenotypes like leaf angle. As such, depth imaging is an economical and rapid method to acquire shoot architecture phenotypes in agriculturally important plants like sorghum to study the genetic basis of complex traits.

Increasing food production is essential to meet the demands of a growing human population, with its rising income levels and nutritional expectations. To address the demand, plant breeders seek new sources of genetic variation to enhance the productivity, sustainability and resilience of crop varieties. Here we launch a high-resolution, open-access research platform to facilitate genome-wide association mapping in rice, a staple food crop. The platform provides an immortal collection of diverse germplasm, a high-density single-nucleotide polymorphism data set tailored for gene discovery, well-documented analytical strategies, and a suite of bioinformatics resources to facilitate biological interpretation. Using grain length, we demonstrate the power and resolution of our new high-density rice array, the accompanying genotypic data set, and an expanded diversity panel for detecting major and minor effect QTLs and subpopulation-specific alleles, with immediate implications for rice improvement. Understanding the link between genotype and phenotype can facilitate efforts by breeders to utilize natural variation and develop new crop varieties. Here the authors present a diverse germplasm collection, a high-density genotyping array and a set of bioinformatic tools to enable association mapping in rice.

Charles Darwin founded root system architecture research in 1880 when he described a root bending with gravity. Curving, elongating, and branching are the three cellular processes in roots that underlie root architecture. Together they determine the distribution of roots through soil and time, and hence the plants’ access to water and nutrients, and anchorage. Most knowledge of these cellular processes comes from seedlings of the model dicotyledon, Arabidopsis, grown in soil-less conditions with single treatments. Root systems in the field, however, face multiple stimuli that interact with the plant genetics to result in the root system architecture. Here we review how soil conditions influence root system architecture; focusing on cereals. Cereals provide half of human calories, and their root systems differ from those of dicotyledons. We find that few controlled-environment studies combine more than one soil stimulus and, those that do, highlight the complexity of responses. Most studies are conducted on seedling roots; those on adult roots generally show low correlations to seedling studies. Few field studies report root and soil conditions. Until technologies are available to track root architecture in the field, soil analyses combined with knowledge of the effects of factors on elongation and gravitropism could be ranked to better predict the interaction between genetics and environment (G×E) for a given crop. Understanding how soil conditions regulate root architecture can be effectively used to design soil management and plant genetics that best exploit synergies from G×E of roots.

Plant organs, such as seeds, are primary sources of food for both humans and animals. Seed size is one of the major agronomic traits that have been selected in crop plants during their domestication. Legume seeds are a major source of dietary proteins and oils. Here, we report a conserved role for the BIG SEEDS1 (BS1) gene in the control of seed size and weight in the model legume Medicago truncatula and the grain legume soybean (Glycine max). BS1 encodes a plant-specific transcription regulator and plays a key role in the control of the size of plant organs, including seeds, seed pods, and leaves, through a regulatory module that targets primary cell proliferation. Importantly, down-regulation of BS1 orthologs in soybean by an artificial microRNA significantly increased soybean seed size, weight, and amino acid content. Our results provide a strategy for the increase in yield and seed quality in legumes.

The genetic gain in yield and quality are two major targets of wheat breeding programs around the world. In this study, a high density genetic map consisting of 10,172 SNP markers identified a total of 43 genomic regions associated with three quality traits, three yield traits and two agronomic traits in hard red spring wheat (HRSW). When compared with six grain shape and size traits, the quality traits showed mostly independent genetic control (~18% common loci), while the yield traits showed moderate association (~53% common loci). Association of genomic regions for grain area (GA) and thousand-grain weight (TGW), with yield suggests that targeting an increase in GA may help enhancing wheat yield through an increase in TGW. Flour extraction (FE), although has a weak positive phenotypic association with grain shape and size, they do not share any common genetic loci. A major contributor to plant height was the Rht8 locus and the reduced height allele was associated with significant increase in grains per spike (GPS) and FE, and decrease in number of spikes per square meter and test weight. Stable loci were identified for almost all the traits. However, we could not find any QTL in the region of major known genes like GPC-B1, Ha, Rht-1, and Ppd-1. Epistasis also played an important role in the genetics of majority of the traits. In addition to enhancing our knowledge about the association of wheat quality and yield with grain shape and size, this study provides novel loci, genetic information and pre-breeding material (combining positive alleles from both parents) to enhance the cultivated gene pool in wheat germplasm. These resources are valuable in facilitating molecular breeding for wheat quality and yield improvement.

Background Asian cultivars were predominantly represented in global rice panel selected for sequencing and to identify novel alleles for drought tolerance. Diverse genetic resources adapted to Indian subcontinent were not represented much in spite harboring useful alleles that could improve agronomic traits, stress resilience and productivity. These rice accessions are valuable genetic resource in developing rice varieties suited to different rice ecosystem that experiences varying drought stress level, and at different crop stages. A core collection of rice germplasm adapted to Southwestern Indian peninsular genotyped using SSR markers and characterized by contrasting water regimes to associate genomic regions for physiological, root traits and yield related traits. Genotyping-By-Sequencing of selected accessions within the diverse panel revealed haplotype variation in genic content within genomic regions mapped for physiological, morphological and root traits. Results Diverse rice panel (99 accessions) were evaluated in field and measurements on plant physiological, root traits and yield related traits were made over five different seasons experiencing varying drought stress intensity at different crop stages. Traits like chlorophyll stability index, leaf rolling, days to 50% flowering, chlorophyll content, root volume and root biomass were identified as best predictors of grain yield under stress. Association mapping revealed genetic variation among accessions and revealed 14 genomic targets associated with different physiological, root and plant production traits. Certain accessions were found to have beneficial allele to improve traits, plant height, root length and spikelet fertility, that contribute to the grain yield under stress. Genomic characterization of eleven accessions revealed haplotype variation within key genomic targets on chromosomes 1, 4, 6 and 11 for potential use as molecular markers to combine drought avoidance and tolerance traits. Genes mined within the genomic QTL intervals identified were prioritized based on tissue specific expression level in publicly available rice transcriptome data. Conclusion The genetic and genomic resources identified will enable combining traits with agronomic value to optimize yield under stress and hasten trait introgression into elite cultivars. Alleles associated with plant height, specific leaf area, root length from PTB8 and spikelet fertility and grain weight from PTB26 can be harnessed in future rice breeding program.

An East Asian winter monsoon proxy record using grain size variations in Chinese loess over the past 900,000 years shows that for up to 20,000 years after the interglacials at 400,000-year intervals, the weak monsoon winds maintain a mild, non-glacial climate at high northern latitudes. Expect 'non-glacial' Arctic climate to persist Qingzhen Hao and colleagues present a record of grain-size variations in the Chinese Loess Plateau — a proxy of variations in the strength of the East Asian winter monsoon — and show that relatively high insolation at 400,000-year intervals held off the inception of the subsequent ice age for about 20,000 years relative to other glacial inceptions. Mechanistically, the extension of warm conditions was probably linked to a weak Siberian high-pressure system associated with a delayed build up of northern ice and snow. The authors speculate that these observations imply that Arctic climate may remain in non-glacial mode for more than 40,000 years, even in the absence of anthropogenic greenhouse gases. Knowledge of the past variability of climate at high northern latitudes during astronomical analogues of the present interglacial 1 may help to inform our understanding of future climate change. Unfortunately, long-term continuous records of ice-sheet variability in the Northern Hemisphere only are scarce because records of benthic 18 O content represent an integrated signal of changes in ice volume in both polar regions 2 . However, variations in Northern Hemisphere ice sheets influence the Siberian High 3 (an atmospheric pressure system), so variations in the East Asian winter monsoon (EAWM)—as recorded in the aeolian dust deposits on the Chinese Loess Plateau—can serve as a useful proxy of Arctic climate variability before the ice-core record begins. Here we present an EAWM proxy record using grain-size variations in two parallel loess sections representative of sequences across the whole of the Chinese Loess Plateau over the past 900,000 years. The results show that during periods of low eccentricity and precessional variability at approximately 400,000-year intervals, the grain-size-inferred intensity of the EAWM remains weak for up to 20,000 years after the end of the interglacial episode of high summer monsoon activity and strong pedogenesis. In contrast, there is a rapid increase in the EAWM after the end of most other interglacials. We conclude that, for both the 400,000-year interglacials, the weak EAWM winds maintain a mild, non-glacial climate at high northern latitudes for much longer than expected from the conventional loess and marine oxygen isotope records. During these times, the less-severe summer insolation minima at 65° N (ref. 4 ) would have suppressed ice and snow accumulation, leading to a weak Siberian High and, consequently, weak EAWM winds.