Genome-Wide Association Studies of Grain Yield Components in Diverse Sorghum Germplasm

Citation: Boyles, R. E., Cooper, E. A., Myers, M. T., Brenton, Z., Rauh, B. L., Morris, G. P., & Kresovich, S. (2016). Genome-Wide Association Studies of Grain Yield Components in Diverse Sorghum Germplasm. Plant Genome, 9(2), 17. doi:10.3835/plantgenome2015.09.0091Grain yield and its primary determinants, grain number and weight, are important traits in cereal crops that have been well studied; however, the genetic basis of and interactions between these traits remain poorly understood. Characterization of grain yield per primary panicle (YPP), grain number per primary panicle (GNP), and 1000-grain weight (TGW) in sorghum [Sorghum bicolor (L.) Moench], a hardy C-4 cereal with a genome size of similar to 730 Mb, was implemented in a diversity panel containing 390 accessions. These accessions were genotyped to obtain 268,830 single-nucleotide polymorphisms (SNPs). Genome-wide association studies (GWAS) were performed to identify loci associated with each grain yield component and understand the genetic interactions between these traits. Genome-wide association studies identified associations across the genome with YPP, GNP, and TGW that were located within previously mapped sorghum QTL for panicle weight, grain yield, and seed size, respectively. There were no significant associations between GNP and TGW that were within 100 kb, much greater than the average linkage disequilibrium (LD) in sorghum. The identification of nonoverlapping loci for grain number and weight suggests these traits may be manipulated independently to increase the grain yield of sorghum. Following GWAS, genomic regions surrounding each associated SNP were mined for candidate genes. Previously published expression data indicated several TGW candidate genes, including an ethylene receptor homolog, were primarily expressed within developing seed tissues to support GWAS. Furthermore, maize (Zea mays L.) homologs of identified TGW candidates were differentially expressed within the seed between small- and large-kernel lines from a segregating maize population

Post head-emergence frost resistance of barley genotypes in the northern grain region of Australia.

Post head-emergence frost causes substantial losses for Australian barley producers. Varieties with improved resistance would have a significant positive impact on Australian cropping enterprises. Five barley genotypes previously tested for reproductive frost resistance in southern Australia were tested, post head-emergence, in the northern grain region of Australia and compared with the typical northern control cultivars, Gilbert and Kaputar. All tested genotypes suffered severe damage to whole heads and stems at plant minimum temperatures less than -8degreesC. In 2003, 2004 and 2005, frost events reaching a plant minimum temperature of ~-6.5degreesC did not result in the complete loss of grain yield. Rather, partial seed set was observed. The control genotype, Gilbert, exhibited seed set that was greater than or equal to that of any genotype in each year, as did Kaputar when tested in 2005. Thus, Gilbert and Kaputar were at least as resistant as any tested genotype. This contrasts with trial results from the southern grain region where Gilbert was reported to be less resistant than Franklin, Amagi Nijo and Haruna Nijo. Hence, rankings for post head-emergence frost damage in the northern grain region differ from those previously reported. These results indicate that Franklin, Amagi Nijo and Haruna Nijo are not likely to provide useful sources of frost resistance or markers to develop improved varieties for the northern grain region of Australia

Season, nitrogen rate, and plant type affect nitrogen uptake and nitrogen use efficiency in rice

Studies were undertaken in the Burdekin River Irrigation Area of northern Australia to improve the efficiency of nitrogen (N) use for rice (Oryza sativa L.) production. The aim was to maximise grain yield by optimising its functional components: N uptake, efficiency of N use for dry matter production (NUEdm), and harvest index (HI). The effiects of season (wet and dry), N rate (0, 70, 140, 210, and 280 kg/ha), and plant type (maturity and stature) on N uptake, NUEdm, and HI were examined in 2 wet and 2 dry seasons. Leaf area development was closely related to N uptake. In the wet season, genotypes had similar rates of increase in leaf area index (LAI) with N uptake but differed in the level of LAI (curves were parallel). In the dry season, the relationship between N uptake and LAI was different for each genotype (curves not parallel). In both seasons cv. Newbonnet generally had a lower LAI per unit N uptake (i.e. leaf area production was not excessive) than cvv. Lemont and Starbonnet. Dry matter production and grain yield were also closely related to N uptake. At low levels of N availability (N uptake <100 kg/ha) tissue N concentrations were low and both total above-ground dry mass (AGDM) and grain yield were linearly related to N uptake. As N availability increased, N uptake and tissue N concentration increased, resulting in a deviation of the AGDM and grain yield curves from the linear at about 100 kg/haN uptake. This finally resulted in AGDM and grain yield plateauing at around 200 kg/ha N uptake. Above this level some factors other than N availability limited yield. Seasonal differences in N uptake, NUEdm, and HI were observed. Seasonal variation in the response of grain yield to N uptake was found. There was a trend for higher N uptake in the absence of fertiliser application in the wet than the dry season, and the recovery fraction was less for N rates >140 kg/ha in all seasons, i.e. fertiliser N uptake efficiency declined with increasing N rate. Nitrogen was used more effectively by the rice crop to produce grain compared with non-grain parts when average daily mean temperatures were lower during the period between panicle initiation and anthesis. Genotypic variation was found in N uptake, NUEdm, and HI. The ability to capture these components in crop improvement programs depends on the extent to which genetic linkages between N uptake and both NUEdm and HI can be broken. While our data suggest that N uptake is generally negatively correlated with both NUEdm and HI, there is some evidence that these linkages can be broken. For example, the fact that HIdid not change with increasing N uptake in Lemont and, to a lesser extent, in Newbonnet suggests that HI does not always decline with increasing N uptake. The example of Newbonnet suggests that, to some extent, it is possible to increase yield by increasing each of the functional components independently within a specific genotype

Functional dynamics of the nitrogen balance of sorghum: I. N demand of vegetative plant parts

Stay-green, an important trait for grain yield of sorghum grown under water limitation, has been associated with a high leaf nitrogen content at the start of grain filling. This study quantifies the N demand of leaves and stems and explores effects of N stress on the N balance of vegetative plant parts of three sorghum hybrids differing in potential crop height. The hybrids were grown under well-watered conditions at three levels of N supply. Vertical profiles of biomass and N% of leaves and stems, together with leaf size and number, and specific leaf nitrogen (SLN), were measured at regular intervals. The hybrids had similar minimum but different critical and maximum SLN, associated with differences in leaf size and N partitioning, the latter associated with differences in plant height. N demand of expanding new leaves was represented by critical SLN, and structural stem N demand by minimum stem N%. The fraction of N partitioned to leaf blades increased under N stress. A framework for N dynamics of leaves and stems is developed that captures effects of N stress and genotype on N partitioning and on critical and maximum SLN