Maize (Zea mays L.) Genome Diversity as Revealed by RNA-Sequencing

Maize is rich in genetic and phenotypic diversity. Understanding the sequence, structural, and expression variation that contributes to phenotypic diversity would facilitate more efficient varietal improvement. RNA based sequencing (RNA-seq) is a powerful approach for transcriptional analysis, assessing sequence variation, and identifying novel transcript sequences, particularly in large, complex, repetitive genomes such as maize. In this study, we sequenced RNA from whole seedlings of 21 maize inbred lines representing diverse North American and exotic germplasm. Single nucleotide polymorphism (SNP) detection identified 351,710 polymorphic loci distributed throughout the genome covering 22,830 annotated genes. Tight clustering of two distinct heterotic groups and exotic lines was evident using these SNPs as genetic markers. Transcript abundance analysis revealed minimal variation in the total number of genes expressed across these 21 lines (57.1% to 66.0%). However, the transcribed gene set among the 21 lines varied, with 48.7% expressed in all of the lines, 27.9% expressed in one to 20 lines, and 23.4% expressed in none of the lines. De novo assembly of RNA-seq reads that did not map to the reference B73 genome sequence revealed 1,321 high confidence novel transcripts, of which, 564 loci were present in all 21 lines, including B73, and 757 loci were restricted to a subset of the lines. RT-PCR validation demonstrated 87.5% concordance with the computational prediction of these expressed novel transcripts. Intriguingly, 145 of the novel de novo assembled loci were present in lines from only one of the two heterotic groups consistent with the hypothesis that, in addition to sequence polymorphisms and transcript abundance, transcript presence/absence variation is present and, thereby, may be a mechanism contributing to the genetic basis of heterosis

Understanding and using quantitative genetic variation

Quantitative genetics, or the genetics of complex traits, is the study of those characters which are not affected by the action of just a few major genes. Its basis is in statistical models and methodology, albeit based on many strong assumptions. While these are formally unrealistic, methods work. Analyses using dense molecular markers are greatly increasing information about the architecture of these traits, but while some genes of large effect are found, even many dozens of genes do not explain all the variation. Hence, new methods of prediction of merit in breeding programmes are again based on essentially numerical methods, but incorporating genomic information. Long-term selection responses are revealed in laboratory selection experiments, and prospects for continued genetic improvement are high. There is extensive genetic variation in natural populations, but better estimates of covariances among multiple traits and their relation to fitness are needed. Methods based on summary statistics and predictions rather than at the individual gene level seem likely to prevail for some time yet

Augmenting the pearl millet core collection for enhancing germplasm utilization in crop improvement

Developing a core collection that represents the diversity of entire collection is an efficient approach to enhance the use of germplasm in crop improvement. Core collections are dynamic and need to be revised when additional germplasm and information become available. In the present study, the pearl millet [Pennisetum glaucum (L.) R. Br.] core collection, consisting of 1600 accessions selected from about 16,000 accessions characterized at the International Crops Research Institute for the Semi-Arid Tropics Genebank by 1998, was augmented by adding 501 accessions representing 4717 accessions assembled and characterized in the past 9 yr. The revised core consists 2094 accessions. (Five duplicate and two male sterile accessions were deleted from original core collection.) A comparison of mean data using Newman-Keuls test, variance using Levene's test, and distribution using χ2 test indicated that the variation in the entire collection of 20,766 accessions was preserved in the revised core collection. A few important phenotypic correlations that may be under coadapted gene complexes were preserved in the revised core collection. The Shannon-Weaver diversity index for different traits was similar in the revised core and entire collection. The revised core collection was observed to be more valuable than the original core as it has sources of resistance for important diseases such as downy mildew. The revised core collection could be a point of entry to the proper exploitation of pearl millet genetic resources for crop improvement

Phenotypic, cytogenetic and spike fertility characterization of a population of male-sterile triticale

Triticale (X Triticosecale Wittmack) is a good cereal for production of flour and feed. A segregating population of triticale was developed from a male-sterile (MS) plant. To determine whether this new source of male sterility in triticale is appropriate for use in breeding programs the expression of the male sterility phenotype was characterized through spike fertility, meiotic behavior, and pollen. Controlled crosses between male-sterile plants and control varieties male-fertile (MF) of triticale were also conducted, and cytological analyses were performed in the F2 and backcross plants. Plants with male-sterile phenotypes displayed reduced spike fertility when compared to plants with male-fertile phenotypes. Compared to male-fertile plants, male-sterile plants exhibited a lower percentage of normal meiotic cells, a reduced meiotic index and reduced pollen viability. The F2 plants had improved pollen fertility when compared to the male-sterile population; however there were no corresponding improvements in the percentage of normal meiotic cells or in the meiotic index. A single generation of backcrosses resulted in an improved meiotic index and increased pollen viability. However, no changes in the percentage of normal meiotic cells were observed. Meiotic instability, which was shown to be inheritable, was the likely cause of male sterility. Therefore, the use of this population in triticale breeding was considered to be inappropriate because it could promote or contribute to the maintenance of meiotic instability, which is commonly observed in this species

A Dynamic and Complex Network Regulates the Heterosis of Yield-Correlated Traits in Rapeseed (Brassica napus L.)

Although much research has been conducted, the genetic architecture of heterosis remains ambiguous. To unravel the genetic architecture of heterosis, a reconstructed F2 population was produced by random intercross among 202 lines of a double haploid population in rapeseed (Brassica napus L.). Both populations were planted in three environments and 15 yield-correlated traits were measured, and only seed yield and eight yield-correlated traits showed significant mid-parent heterosis, with the mean ranging from 8.7% (branch number) to 31.4% (seed yield). Hundreds of QTL and epistatic interactions were identified for the 15 yield-correlated traits, involving numerous variable loci with moderate effect, genome-wide distribution and obvious hotspots. All kinds of mode-of-inheritance of QTL (additive, A; partial-dominant, PD; full-dominant, D; over-dominant, OD) and epistatic interactions (additive × additive, AA; additive × dominant/dominant × additive, AD/DA; dominant × dominant, DD) were observed and epistasis, especially AA epistasis, seemed to be the major genetic basis of heterosis in rapeseed. Consistent with the low correlation between marker heterozygosity and mid-parent heterosis/hybrid performance, a considerable proportion of dominant and DD epistatic effects were negative, indicating heterozygosity was not always advantageous for heterosis/hybrid performance. The implications of our results on evolution and crop breeding are discussed

Herbicide-Resistant Crops: Utilities and Limitations for Herbicide-Resistant Weed Management

Since 1996, genetically modified herbicide-resistant (HR) crops, particularly glyphosate-resistant (GR) crops, have transformed the tactics that corn, soybean, and cotton growers use to manage weeds. The use of GR crops continues to grow, but weeds are adapting to the common practice of using only glyphosate to control weeds. Growers using only a single mode of action to manage weeds need to change to a more diverse array of herbicidal, mechanical, and cultural practices to maintain the effectiveness of glyphosate. Unfortunately, the introduction of GR crops and the high initial efficacy of glyphosate often lead to a decline in the use of other herbicide options and less investment by industry to discover new herbicide active ingredients. With some exceptions, most growers can still manage their weed problems with currently available selective and HR crop-enabled herbicides. However, current crop management systems are in jeopardy given the pace at which weed populations are evolving glyphosate resistance. New HR crop technologies will expand the utility of currently available herbicides and enable new interim solutions for growers to manage HR weeds, but will not replace the long-term need to diversify weed management tactics and discover herbicides with new modes of action. This paper reviews the strengths and weaknesses of anticipated weed management options and the best management practices that growers need to implement in HR crops to maximize the long-term benefits of current technologies and reduce weed shifts to difficult-to-control and HR weeds

Detailed Analysis of a Contiguous 22-Mb Region of the Maize Genome

Most of our understanding of plant genome structure and evolution has come from the careful annotation of small (e.g., 100 kb) sequenced genomic regions or from automated annotation of complete genome sequences. Here, we sequenced and carefully annotated a contiguous 22 Mb region of maize chromosome 4 using an improved pseudomolecule for annotation. The sequence segment was comprehensively ordered, oriented, and confirmed using the maize optical map. Nearly 84% of the sequence is composed of transposable elements (TEs) that are mostly nested within each other, of which most families are low-copy. We identified 544 gene models using multiple levels of evidence, as well as five miRNA genes. Gene fragments, many captured by TEs, are prevalent within this region. Elimination of gene redundancy from a tetraploid maize ancestor that originated a few million years ago is responsible in this region for most disruptions of synteny with sorghum and rice. Consistent with other sub-genomic analyses in maize, small RNA mapping showed that many small RNAs match TEs and that most TEs match small RNAs. These results, performed on ∼1% of the maize genome, demonstrate the feasibility of refining the B73 RefGen_v1 genome assembly by incorporating optical map, high-resolution genetic map, and comparative genomic data sets. Such improvements, along with those of gene and repeat annotation, will serve to promote future functional genomic and phylogenomic research in maize and other grasses

Lengthening of maize maturity time is not a widespread climate change adaptation strategy in the US Midwest

Increasing temperatures in the US Midwest are projected to reduce maize yields because warmer temperatures hasten reproductive development and, as a result, shorten the grain fill period. However, there is widespread expectation that farmers will mitigate projected yield losses by planting longer season hybrids that lengthen the grain fill period. Here, we ask: (a) how current hybrid maturity length relates to thermal availability of the local climate, and (b) if farmers are shifting to longer season hybrids in response to a warming climate. To address these questions, we used county‐level Pioneer brand hybrid sales (Corteva Agriscience) across 17 years and 650 counties in 10 Midwest states (IA, IL, IN, MI, MN, MO, ND, OH, SD, and WI). Northern counties were shown to select hybrid maturities with growing degree day (GDD°C) requirements more closely related to the environmentally available GDD compared to central and southern counties. This measure, termed “thermal overlap,” ranged from complete 106% in northern counties to a mere 63% in southern counties. The relationship between thermal overlap and latitude was fit using split‐line regression and a breakpoint of 42.8°N was identified. Over the 17‐years, hybrid maturities shortened across the majority of the Midwest with only a minority of counties lengthening in select northern and southern areas. The annual change in maturity ranged from −5.4 to 4.1 GDD year−1 with a median of −0.9 GDD year−1. The shortening of hybrid maturity contrasts with widespread expectations of hybrid maturity aligning with magnitude of warming. Factors other than thermal availability appear to more strongly impact farmer decision‐making such as the benefit of shorter maturity hybrids on grain drying costs, direct delivery to ethanol biorefineries, field operability, labor constraints, and crop genetics availability. Prediction of hybrid choice under future climate scenarios must include climatic factors, physiological‐genetic attributes, socio‐economic, and operational constraints