Resequencing of two elite sorghum (Sorghum bicolor (L.) Moench) hybrid parent lines reveals distinctly different genome-wide variation models

Genetic structure of 142 parent lines of sorghum [Sorghum bicolor (L.) Moench] was analyzed using model-based approach based on SSR markers. Forty-one selected from 103 SSR markers were used to analyze the parent lines, which generated 189 alleles revealed by each marker ranging from 2 to 11 with an average of 4.6 per marker. The polymorphic information content (PIC) value was 0.543 with a range of 0.089 to 0.850. All the parent lines were assigned to 7 subgroups, named Kafir, Kaoliang, Feterita, Shallu, Hegari, Milo and Durra. Parent lines without clear pedigree record were clustered into their corresponding groups, and genetic components of each line were estimated by Q-values. Information of this study would be useful for breeders to conclude their genetic background and select appropriate parents for germplasm improvement and hybrid breeding, and thus improve the efficiency of breeding programs.

Sorghum (Sorghum bicolor L.) is the fifth among the world’s most important crops, mostly grown in arid and semiarid regions of the world. In sorghum, mounting commercial single cross hybrids, owing to their morphological homogeny, has been more preferred by growers. Hence, cytoplasmic male sterility (CMS) has emerged as a more prominent gifted approach to achieve sustainability in crop productivity systems due to its substantial contribution in the production of crop hybrids by practically deceiving the need of removal of anthers, resulting in generation of superior F1 hybrids. Owing to the ordinariness of multiple sources of CMS, the observation of shrewd level of instability and the frequency of fertility restorer genes in the germplasm make sorghum a particularly fascinating system for the investigation of male sterility and fertility restoration. Moreover, rapid isolation of potential restorers, precise introgression of rf genes to diverse genetic backgrounds, genetic purity assurance among parents and hybrids and swift prejudice among parental lines constitute crucial steps in cytoplasmic male sterility-based heterosis breeding. Here, we prospectively review the cytoplasmic male sterility (CMS) and its relevance to hybrid breeding in sorghum with potential impending on cytoplasmic–nuclear genomic interactions, marker-assisted selection (MAS) ensuring the eventual combination of multiple resistance with yield stability, omic technologies ensuring elaborative analysis of sterility and fertility retrieval functionaries like introduction of novel sterility inducing orfs.KeywordsCytoplasmFertility restorationGenomeHeterosisHybridMale sterilityPollen

Genetic diversity is key for breeding population development, hybrid breeding, heterotic grouping and genetic analysis, among others. The objective of this study was to examine genetic interrelationships among elite sorghum genotypes bred for resistance to Striga hermonthica Del. Benth and S. asiatica (L.) Kuntze and compatible with a biological control agent Fusarium oxysporum f. sp. strigae (FOS) against Striga using 22 polymorphic simple sequence repeat (SSR) or microsatellite markers. The number of alleles per locus detected by the markers varied from 2 to 7 with a mean value of 4.23. The polymorphic information content (PIC) of the SSR markers ranged from 0.15 to 0.84 with a mean of 0.57 showing moderate discriminatory power of the primers. The neighbour-joining clustering algorithm classified the genotypes into three main groups, revealing narrow to moderate variations existing among the test genotypes. Overall, the genetic diversity revealed by the study will be useful for designed crosses and pyramiding of broad-based resistance genes to control Striga for sustainable sorghum production.

Hybrid vigor (heterosis) has been used as a breeding technique for crop improvement to achieve enhanced biomass production, but the physiological mechanisms underlying heterosis remain poorly understood. In this study, to find a clue to the enhancement of biomass production by heterosis, we systemically evaluated the effect of heterosis on the growth rate and photosynthetic efficiency in sorghum hybrid [Sorghum bicolor (L.) Moench cv. Tentaka] and its parental lines (restorer line and maintainer line). The final biomass of Tentaka was 10-14 times greater than that of the parental lines grown in an experimental field, but the relative growth rate during the vegetative growth stage did not differ. Tentaka exhibited a relatively enlarged leaf area with lower leaf nitrogen content per leaf area (Narea). When the plants were grown hydroponically at different N levels, daily CO2 assimilation per leaf area (A) increased with Narea, and the ratio of A to Narea (N-use efficiency) was higher in the plants grown at low N levels but not different between Tentaka and the parental lines. The relationships between the CO2 assimilation rate, the amounts of photosynthetic enzymes, including ribulose-1,5-bisphosphate carboxylase/oxygenase, phosphoenolpyruvate carboxylase and pyruvate phosphate dikinase, Chl and Narea did not differ between Tentaka and the parental lines. Thus, Tentaka tended to exhibit enlargement of leaf area with lower N content, leading to a higher N-use efficiency for CO2 assimilation, but the photosynthetic properties did not differ. The greater biomass in Tentaka was mainly due to the prolonged vegetative growth period.

The commercial exploitation of heterosis or hybrid vigor through the development and cultivation of hybrid cultivars is one of the landmark achievements in plant breeding. Ever since the two pioneering publications by George H. Shull 100 years ago, in which he scientifically described heterosis and laid the foundation of modern hybrid breeding in maize, the exploitation of heterosis in crop and tree species has greatly expanded and the acreage under hybrid cultivars has steadily increased. Thus, hybrid breeding has made commendable contributions in meeting the food, feed, and fiber needs of the burgeoning population of the world, and benefitted farmers and consumers. It also promoted the development of a viable seed industry, which was a tremendous stimulus for the research in plant breeding. The overwhelming importance of heterosis attracted many scientists to study the underlying genetic causes of this unique phenomenon. Vast data sets were generated and analyzed in different disciplines. To compile and discuss the accumulated information, two international conferences were organized in the past: The first conference was held in 1950 at Iowa State College in Ames and lasted for 4 weeks. The second conference was organized in 1997 by CIMMYT in Mexico City. Both conferences proved to be landmarks in research on heterosis and its exploitation in plant breeding. In recent years, there have been new developments in agriculture. On one hand, intensive agriculture is adversely affecting the natural resources and the arable land available for food production is decreasing with the increasing demand of plants for industrial purposes and renewable resources of energy. On the other hand, our needs for food and feed production are increasing, because of an ever growing population and improving living standards. Further, future agriculture is expected to face serious challenges due to the impending climate changes. Consequently, serious concerns are being expressed about the food security of our planet. A viable option to meet the increasing demands is the enhancement of productivity per unit of resources on a sustainable basis. In this scenario, optimal exploitation of heterosis can play a key role. It enables plant breeders to provide cultivars possessing high genetic potential. A better understanding of the causes underlying heterosis will facilitate the development of new breeding approaches for rapid and efficient exploitation of heterosis. The recent advances in genomics, bioinformatics and related fields have provided researchers with novel tools and approaches to investigate heterosis. Multidisciplinary teams of scientists are working on their application to link the new results for a better understanding of heterosis at various biological levels (DNA, mRNA, proteins and metabolites). These advances have expanded the disciplinary domain and knowledge at a rapid pace. Therefore, the University of Hohenheim considered it appropriate to organize and host a third international conference on ‘‘Heterosis in Plants’’ in Stuttgart, Germany, from 7 to 9 September 2009. The main aims of the conference were (1) to summarize the progress in theory and experimental studies on heterosis at different biological levels during the past 12 years, (2) to promote a better understanding of the biological processes underlying heterosis and (3) to stimulate further advances in the exploitation of heterosis in plant breeding by the application of new genomic tools. A. E. Melchinger (&) Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, 70593 Stuttgart, Germany e-mail: melchinger@uni-hohenheim.de

There are many moving parts involved in developing and taking a new commercial hybrid to market. Sorghum [Sorghum bicolor (L.) Moench] hybrid development involves development of parental lines based on a cytoplasmic male sterile system including the pollen parent (R-line) and seed parents (A- and B-lines). New parental lines are developed by recombining existing elite parental lines to create new breeding populations or by adding specific traits of interest to existing parental lines by crossing elite lines with donor parents. Molecular markers are utilized to identify plants with particular traits of interest during parental line development. Newly developed parental lines are crossed together or with other elite parental lines to create new hybrid combinations. New hybrid combinations are evaluated in target geographies for improved yield, good agronomics, and specific traits of interest. Multi-year, multi-location evaluations are used to identify hybrid entries with improved yield, stable performance, and good agronomics. Evaluation of the parental lines involved in these new hybrids helps establish the produceability and potential cost of goods which have direct impact on the potential commercial release of new hybrid products.

Heterosis refers to a quantitative phenomenon in which F1 hybrid trait values exceed the mean of the parental values in a positive direction. Generally, it is dependent on a high degree of heterozygosity, which is maintained in hybrid breeding by developing parental lines in separate, genetically distinct heterotic groups. The mobility of small RNAs (sRNAs) that mediate epigenetic regulation of gene expression renders them promising candidates for modulating the action of combined diverse genomes in trans–and evidence already indicates their contribution to transgressive phenotypes. By sequencing small RNA libraries of a panel of 21 maize parental inbred lines we found a low overlap of 35% between the sRNA populations from both distinct heterotic groups. Surprisingly, in contrast to genetic or gene expression variation, parental sRNA expression variation is negatively correlated with grain yield (GY) heterosis. Among 0.595 million expressed sRNAs, we identified 9,767, predominantly 22- and 24-nt long sRNAs, which showed an association of their differential expression between parental lines and GY heterosis of the respective hybrids. Of these sRNAs, 3,485 or 6,282 showed an association with high or low GY heterosis, respectively, thus the low heterosis associated group prevailing at 64%. The heterosis associated sRNAs map more frequently to genes that show differential expression between parental lines than reference sets. Together these findings suggest that trans-chromosomal actions of sRNAs in hybrids might add up to a negative contribution in heterosis formation, mediated by unfavorable gene expression regulation. We further revealed an exclusive accumulation of 22-nt sRNAs that are associated with low GY heterosis in pericentromeric genomic regions. That recombinational suppression led to this enrichment is indicated by its close correlation with low recombination rates. The existence of this enrichment, which we hypothesize resulted from the separated breeding of inbred lines within heterotic groups, may have implications for hybrid breeding strategies addressing the recombinational constraints characteristic of complex crop genomes.

Heterosis is a crucial factor in enhancing crop yield, particularly in sorghum (Sorghum bicolor ). This research utilised six sorghum restorer lines, six sorghum sterile lines, and 36 hybrid combinations created through the NCII incomplete double-row hybridisation method. We evaluated the performance of F1 generation hybrids for leaf photosynthesis-related parameters, carbon metabolism-related enzymes, and their correlation with yield traits during the flowering stage. Results showed that hybrid sorghum exhibited significant high-parent heterosis in net photosynthetic rate (P n ), transpiration rate (T r ), stomatal conductance (G s ), apparent leaf meat conductance (AMC), ribulose-1,5-bisphosphate (RuBP) carboxylase, phosphoenolpyruvate (PEP) carboxylase, and sucrose phosphate synthase (SPS). Conversely, inter-cellular carbon dioxide concentration (C i ), instantaneous water uses efficiency (WUE), and sucrose synthase (SuSy) displayed mostly negative heterosis. Traits such as 1000-grain weight (TGW), grain weight per spike (GWPS), and dry matter content (DMC) exhibited significant high-parent heterosis, with TGW reaching the highest value of 82.54%. P n demonstrated positive correlations with T r , C i , G s , RuBP carboxylase, PEP carboxylase, GWPS, TGW, and DMC, suggesting that T r , C i , and G s could aid in identifying high-photosynthesis sorghum varieties. Concurrently, P n could help select carbon-efficient sorghum varieties due to its close relationship with yield. Overall, the F1 generation of sorghum hybrids displayed notable heterosis during anthesis. Combined with field performance, P n at athesis can serve as a valuable indicator for early prediction of the yield potential of the F1 generation of sorghum hybrids and for screening carbon-efficient sorghum varieties.

Embryonic numerical and structural chromosomal abnormalities are the most common cause of early pregnancy loss. However, the role of submicroscopic copy-number variations (CNVs) in early pregnancy loss is unclear, and little is known about the critical regions and candidate genes for miscarriage, because of the large size of structural chromosomal abnormalities. The aim of this study was to identify potential miscarriage-associated submicroscopic CNVs and critical regions of large CNVs as well as candidate genes for miscarriage. Over a 5-year period, 5180 fresh miscarriage specimens were investigated using quantitative fluorescent polymerase chain reaction/CNV sequencing or chromosomal microarray analysis. Statistically significant submicroscopic CNVs were identified by comparing the frequency of recurrent submicroscopic CNVs between cases and a published control cohort. Furthermore, genes within critical regions of miscarriage-associated CNVs were prioritized by integrating the Residual Variation Intolerance Score and the human gene expression dataset for identification of potential miscarriage candidate genes. Results without significant maternal-cell contamination were obtained in 5003 of the 5180 (96.6%) cases. Clinically significant chromosomal abnormalities were identified in 59.1% (2955/5003) of these cases. Three recurrent submicroscopic CNVs (microdeletions in 22q11.21, 2q37.3 and 9p24.3p24.2) were significantly more frequent in miscarriage cases, and were considered to be associated with miscarriage. Moreover, 44 critical regions of large CNVs were observed, including 14 deletions and 30 duplications. There were 309 genes identified as potential miscarriage candidate genes through gene-prioritization analysis. We identified potential miscarriage candidate CNVs and genes. These data demonstrate the importance of CNVs in the etiology of miscarriage and highlight the importance of ongoing analysis of CNVs in the study of miscarriage. Copyright © 2019 ISUOG. Published by John Wiley & Sons Ltd.

To detect copy number variants (CNVs) in patients with congenital heart defects (CHD) and identify potential novel candidate genes involved in CHD pathogenesis. CHD are the most common congenital anomalies....

Sorghum is one of the most widely preferred and cultivated crops in Ethiopia. It is grown for food and feed components. In the developed world, exploitation of heterosis in most crops (Maize, Sorghum, Rice, etc.) is high. There is a clear need to develop sorghum hybrids in Ethiopia to improve their livelihood by increasing sorghum production and productivity. One of the strategies for increasing sorghum yield is through the exploitation of heterosis because sorghum hybrids are high yielder than OPV lines. Properly selected sorghum hybrids can help growers to increase yield, use less water, reduce lodging losses, increase feed quality, and manage maturation time. In Ethiopia, the National Sorghum Research Program runs a multiple technology development work in Ethiopia with the collaboration of International and National Institutions and Universities. One of the oversea collaborative Universities is Purdue University and the Sorghum program received sorghum hybrids to evaluate their performance across sorghum growing dry lowland areas. A total of 35 sorghum hybrid genotypes were introduced and evaluated at six sorghum growing lowland areas of Ethiopia including two recently released hybrid check in 2014. Based on the experimental data submitted to national variety releasing committee, candidate 9187 has been approved for farmers and commercial seed producers in 2018; it is named ESH-5. This hybrid variety is released with a merit of seed color, over all agronomic performance, head shape and yield superior to the recently released hybrid check by 11% yield advantage. Key words: Hybrid, heritability, sorghum, stability.

Background/Aims: In addition to genome-wide association studies (GWAS), height-associated genes may be uncovered by studying individuals with extreme short or tall stature. Methods: Genome-wide analysis for copy number variants (CNVs), using single nucleotide polymorphism (SNP) arrays, was performed in 49 index cases born small for gestational age with persistent short stature. Segregation analysis was performed, and genes in CNVs were compared with information from GWAS, gene expression in rodents' growth plates, and published information. Results: CNVs were detected in 13 cases. In 5 children a known cause of short stature was found: UPD7, UPD14, a duplication of the SHOX enhancer region, an IGF1R deletion, and a 22q11.21 deletion. In the remaining 8 cases, potential pathogenic CNVs were detected, either de novo (n = 1), segregating (n = 2), or not segregating with short stature (n = 5). Bioinformatic analysis of the de novo and segregating CNVs suggested that HOXD4, AGPS, PDE11A, OSBPL6, PRKRA and PLEKHA3, and possibly DGKB and TNFRSF11B are potential candidate genes. A SERPINA7 or NRK defect may be associated with an X-linked form of short stature. Conclusion: SNP arrays detected 5 known causes of short stature with prenatal onset and suggested several potential candidate genes.

Grain sorghum (Sorghum bicolor L. moench) stands as a globally significant cereal crop but the adversity of pre-harvest sprouting (PHS) caused by reduced grain dormancy and moist conditions prior to harvest remains unsolved. Here, we identified a dormancy QTL using a Redlan×IS9530 RIL population, where parent lines are low in tannins and early flowering but otherwise contrasting in grain dormancy and plant height. We phenotyped this population in 2 years with informative PHS-related traits (grain germination index, embryo sensitivity to abscisic acid and in one year the actual natural sprouting), revealing a robust dormancy QTL in chromosome 9 (qDOR-9). This signal overlapped with associations found for plant height (caused by the dw1 locus, used for decades in sorghum improvement) and time to flowering. The effect of qDOR-9 was validated with independent near isogenic lines carrying the IS9530 "dormant" allele while maintaining the Redlan dw1 "short" allele. Additional analyses on Yellow Milo, from which the dw1 allele originated, implied that a low dormancy allele close to dw1 was introduced to Redlan-as well as to many other currently productive lines-by breeding efforts aimed at decreasing plant height, thus illustrating a new instance of genome erosion canalised by crop breeding. However, the introgression of qDOR-9 could enhance PHS tolerance in cultivated dw1-carrying backgrounds without affecting plant stature.

Genetic studies have identified numerous genes reproducibly associated with asthma, yet these studies have focussed almost entirely on single nucleotide polymorphisms (SNPs), and virtually ignored another highly prevalent form of genetic variation: Copy Number Variants (CNVs). To survey the prevalence of CNVs in genes previously associated with asthma, and to assess whether CNVs represent the functional asthma-susceptibility variants at these loci. We genotyped 383 asthmatic trios participating in the Childhood Asthma Management Program (CAMP) using a competitive genomic hybridization (CGH) array designed to interrogate 20 092 CNVs. To ensure comprehensive assessment of all potential asthma candidate genes, we purposely used liberal asthma gene inclusion criteria, resulting in consideration of 270 candidate genes previously implicated in asthma. We performed statistical testing using FBAT-CNV. Copy number variation in asthma candidate genes was prevalent, with 21% of tested genes residing near or within one of 69 CNVs. In six instances, the complete candidate gene sequence resides within the CNV boundaries. On average, asthmatic probands carried six asthma-candidate CNVs (range 1-29). However, the vast majority of identified CNVs were of rare frequency (< 5%) and were not statistically associated with asthma. Modest evidence for association with asthma was observed for 2 CNVs near NOS1 and SERPINA3. Linkage disequilibrium analysis suggests that CNV effects are unlikely to explain previously detected SNP associations with asthma. Although a substantial proportion of asthma-susceptibility genes harbour polymorphic CNVs, the majority of these variants do not confer increased asthma risk. The lack of linkage disequilibrium (LD) between CNVs and asthma-associated SNPs suggests that these CNVs are unlikely to represent the functional variant responsible for most known asthma associations.

BackgroundHeterotaxy (Htx) syndrome comprises a class of congenital disorders resulting from malformations in left-right body patterning. Approximately 90% of patients with heterotaxy have serious congenital heart diseases; as a result, the survival rate and outcomes of Htx patients are not satisfactory. However, the underlying etiology and mechanisms in the majority of Htx cases remain unknown. The aim of this study was to investigate the function of rare copy number variants (CNVs) in the pathogenesis of Htx.MethodsWe collected 63 sporadic Htx patients with congenital heart defects and identified rare CNVs using an Affymetrix CytoScan HD microarray and real-time polymerase chain reaction. Potential candidate genes associated with the rare CNVs were selected by referring to previous literature related to left-right development. The expression patterns and function of candidate genes were further analyzed by whole mount in situ hybridization, morpholino knockdown, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9)-mediated mutation, and over-expressing methods with zebrafish models.ResultsNineteen rare CNVs were identified for the first time in patients with Htx. These CNVs include 5 heterozygous genic deletions, 4 internal genic duplications, and 10 complete duplications of at least one gene. Further analyses of the 19 rare CNVs identified six novel potential candidate genes (NUMB, PACRG, TCTN2, DANH10, RNF115, and TTC40) linked to left-right patterning. These candidate genes exhibited early expression patterns in zebrafish embryos. Functional testing revealed that downregulation and over-expression of five candidate genes (numb, pacrg, tctn2, dnah10, and rnf115) in zebrafish resulted in disruption of cardiac looping and abnormal expression of lefty2 or pitx2, molecular markers of left-right patterning.ConclusionsOur findings show that Htx with congenital heart defects in some sporadic patients may be attributed to rare CNVs. Furthermore, DNAH10 and RNF115 are Htx candidate genes involved in left-right patterning which have not previously been reported in either humans or animals. Our results also advance understanding of the genetic components of Htx.