Showing papers on "Plant breeding published in 2019"

Breeding improves wheat productivity under contrasting agrochemical input levels

Abstract: The world cropping area for wheat exceeds that of any other crop, and high grain yields in intensive wheat cropping systems are essential for global food security. Breeding has raised yields dramatically in high-input production systems; however, selection under optimal growth conditions is widely believed to diminish the adaptive capacity of cultivars to less optimal cropping environments. Here, we demonstrate, in a large-scale study spanning five decades of wheat breeding progress in western Europe, where grain yields are among the highest worldwide, that breeding for high performance in fact enhances cultivar performance not only under optimal production conditions but also in production systems with reduced agrochemical inputs. New cultivars incrementally accumulated genetic variants conferring favourable effects on key yield parameters, disease resistance, nutrient use efficiency, photosynthetic efficiency and grain quality. Combining beneficial, genome-wide haplotypes could help breeders to more efficiently exploit available genetic variation, optimizing future yield potential in more sustainable production systems.

Benefits of Condensed Tannins in Forage Legumes Fed to Ruminants: Importance of Structure, Concentration, and Diet Composition

Abstract: Condensed tannins (CTs) account for up to 20% of the dry matter in forage legumes used as ruminant feeds. Beneficial animal responses to CTs have included improved growth, milk and wool production, fertility, and reduced methane emissions and ammonia volatilization from dung or urine. Most important is the ability of such forages to combat the effects of gastrointestinal parasitic nematodes. Inconsistent animal responses to CTs were initially attributed to concentration in the diet, but recent research has highlighted the importance of their molecular structures, as well as concentration, and also the composition of the diet containing the CTs. The importance of CT structural traits cannot be underestimated. Interdisciplinary research is the key to unraveling the relationships between CT traits and bioactivities and will enable future on-farm exploitation of these natural plant compounds. Research is also needed to provide plant breeders with guidelines and screening tools to optimize CT traits, in both the forage and the whole diet. In addition, improvements are needed in the competitiveness and agronomic traits of CT-containing legumes and our understanding of options for their inclusion in ruminant diets. Farmers need varieties that are competitive in mixed swards and have predictable bioactivities. This review covers recent results from multidisciplinary research on sainfoin (Onobrychis Mill. spp.) and provides an overview of current developments with several other tanniniferous forages. Tannin chemistry is now being linked with agronomy, plant breeding, animal nutrition, and parasitology. The past decade has yielded considerable progress but also generated more questions — an enviable consequence of new knowledge!

Extensive intraspecific gene order and gene structural variations in upland cotton cultivars.

Abstract: Multiple cotton genomes (diploid and tetraploid) have been assembled. However, genomic variations between cultivars of allotetraploid upland cotton (Gossypium hirsutum L.), the most widely planted cotton species in the world, remain unexplored. Here, we use single-molecule long read and Hi-C sequencing technologies to assemble genomes of the two upland cotton cultivars TM-1 and zhongmiansuo24 (ZM24). Comparisons among TM-1 and ZM24 assemblies and the genomes of the diploid ancestors reveal a large amount of genetic variations. Among them, the top three longest structural variations are located on chromosome A08 of the tetraploid upland cotton, which account for ~30% total length of this chromosome. Haplotype analyses of the mapping population derived from these two cultivars and the germplasm panel show suppressed recombination rates in this region. This study provides additional genomic resources for the community, and the identified genetic variations, especially the reduced meiotic recombination on chromosome A08, will help future breeding.

Genetic Diversity and Population Structure of a Camelina sativa Spring Panel.

Abstract: There is a need to explore renewable alternatives (e.g., biofuels) that can produce energy sources to help reduce the reliance on fossil oils. In addition, the consumption of fossil oils adversely affects the environment and human health via the generation of waste water, greenhouse gases, and waste solids. Camelina sativa, originated from southeastern Europe and southwestern Asia, is being re-embraced as an industrial oilseed crop due to its high seed oil content (36-47%) and high unsaturated fatty acid composition (>90%), which are suitable for jet fuel, biodiesel, high-value lubricants and animal feed. C. sativa's agronomic advantages include short time to maturation, low water and nutrient requirements, adaptability to adverse environmental conditions and resistance to common pests and pathogens. These characteristics make it an ideal crop for sustainable agricultural systems and regions of marginal land. However, the lack of genetic and genomic resources has slowed the enhancement of this emerging oilseed crop and exploration of its full agronomic and breeding potential. Here, a core of 213 spring C. sativa accessions was collected and genotyped. The genotypic data was used to characterize genetic diversity and population structure to infer how natural selection and plant breeding may have affected the formation and differentiation within the C. sativa natural populations, and how the genetic diversity of this species can be used in future breeding efforts. A total of 6,192 high-quality single nucleotide polymorphisms (SNPs) were identified using genotyping-by-sequencing (GBS) technology. The average polymorphism information content (PIC) value of 0.29 indicate moderate genetic diversity for the C. sativa spring panel evaluated in this report. Population structure and principal coordinates analyses (PCoA) based on SNPs revealed two distinct subpopulations. Sub-population 1 (POP1) contains accessions that mainly originated from Germany while the majority of POP2 accessions (>75%) were collected from Eastern Europe. Analysis of molecular variance (AMOVA) identified 4% variance among and 96% variance within subpopulations, indicating a high gene exchange (or low genetic differentiation) between the two subpopulations. These findings provide important information for future allele/gene identification using genome-wide association studies (GWAS) and marker-assisted selection (MAS) to enhance genetic gain in C. sativa breeding programs.

Overexpression of zmm28 increases maize grain yield in the field

Abstract: Increasing maize grain yield has been a major focus of both plant breeding and genetic engineering to meet the global demand for food, feed, and industrial uses. We report that increasing and extending expression of a maize MADS-box transcription factor gene, zmm28, under the control of a moderate-constitutive maize promoter, results in maize plants with increased plant growth, photosynthesis capacity, and nitrogen utilization. Molecular and biochemical characterization of zmm28 transgenic plants demonstrated that their enhanced agronomic traits are associated with elevated plant carbon assimilation, nitrogen utilization, and plant growth. Overall, these positive attributes are associated with a significant increase in grain yield relative to wild-type controls that is consistent across years, environments, and elite germplasm backgrounds.

Impacts of maize domestication and breeding on rhizosphere microbial community recruitment from a nutrient depleted agricultural soil.

Abstract: Maize domestication and breeding have resulted in drastic and well documented changes in aboveground traits, but belowground effects on root system functioning and rhizosphere microbial communities remain poorly understood, despite their critical importance for nutrient and water acquisition. We investigated the rhizosphere microbial community composition and structure of ten Zea mays accessions along an evolutionary transect (two teosinte, three inbred maize lines, and five modern maize hybrids) grown in nutrient depleted soil from a low input agricultural system. Microbial community analysis revealed significant differences in community composition between soil compartments (proximal vs. distal rhizosphere) and between plant genetic groups (teosinte, inbred, and modern hybrid). Only a small portion of the microbial community was differentially selected across plant genetic groups: 3.7% of prokaryotic community members and 4.9% of fungal community members were significantly associated with a specific plant genetic group. Indicator species analysis showed the greatest differentiation between modern hybrids and the other two plant genetic groups. Co-occurrence network analysis revealed that microbial co-occurrence patterns of the inbred maize lines' rhizosphere were significantly more similar to those of the teosintes than to the modern hybrids. Our results suggest that advances in hybrid development significantly impacted rhizosphere microbial communities and network assembly.

Integrating Molecular Markers and Environmental Covariates To Interpret Genotype by Environment Interaction in Rice (Oryza sativa L.) Grown in Subtropical Areas

Abstract: Understanding the genetic and environmental basis of genotype × environment interaction (G×E) is of fundamental importance in plant breeding. If we consider G×E in the context of genotype × year interactions (G×Y), predicting which lines will have stable and superior performance across years is an important challenge for breeders. A better understanding of the factors that contribute to the overall grain yield and quality of rice (Oryza sativa L.) will lay the foundation for developing new breeding and selection strategies for combining high quality, with high yield. In this study, we used molecular marker data and environmental covariates (EC) simultaneously to predict rice yield, milling quality traits and plant height in untested environments (years), using both reaction norm models and partial least squares (PLS), in two rice breeding populations (indica and tropical japonica). We also sought to explain G×E by differential quantitative trait loci (QTL) expression in relation to EC. Our results showed that PLS models trained with both molecular markers and EC gave better prediction accuracies than reaction norm models when predicting future years. We also detected milling quality QTL that showed a differential expression conditional on humidity and solar radiation, providing insight for the main environmental factors affecting milling quality in subtropical and temperate rice growing areas.

Multi-dimensional evaluation of response to salt stress in wheat.

Abstract: Soil salinity is a major threat to crop production worldwide. The global climate change is further accelerating the process of soil salinization, particularly in dry areas of the world. Increasing genetic variability of currently used wheat varieties by introgression of exotic alleles/genes from related progenitors' species in breeding programs is an efficient approach to overcome limitations due to the absence of valuable genetic diversity in elite cultivars. Synthetic hexaploid wheat (SHW) is widely regarded as donor of favourable exotic alleles to improve tolerance against biotic and abiotic stresses such as salinity stress. In this study, synthetic backcross lines (SBLs) winter wheat population "Z86", derived from crosses involving synthetic hexaploid wheat Syn86L with German elite winter wheat cultivar Zentos, was evaluated for salinity tolerance at different developmental stages under controlled and field conditions in three growing seasons. High genetic variability was detected across the SBLs and their parents at various growth stages under controlled as well as under salt stress field trials. Greater performance of Zentos over Syn86L was detected at germination stage across all salt treatments and with respect to shoot dry weight (SDW) and root dry weight (RDW) at seedling stage. Whereas for the root length (RL) and the shoot length (SL) Syn86L surpassed the elite cultivar and most of the progenies. Our experiments revealed for almost all traits that some genotypes among the SBLs showed higher performance than their parents. Furthermore, positive transgressive segregations were detected among the SBLs for germination at high salinity levels, as well as for RDW and SDW at seedling stage. Therefore, the studied Z86 population is a suitable population for assessment of salinity stress on morphological and physiological traits at different plant growth stages. The identified SBLs provide a valuable source for genetic gain through recombination of superior alleles that can be directly applied in breeding programs for efficiently breeding cultivars with improved salinity tolerance and desired agronomic traits.

Stability and G × E analysis of zinc-biofortified rice genotypes evaluated in diverse environments

Abstract: Rice is the major staple food and source of energy in Asia, particularly in the Philippines. Most of the popular, high-yielding rice varieties lack sufficient amount of micronutrients to meet daily human requirements. Micronutrient deficiencies are a major health burden globally and can cause severe health problems. In the Philippines, nearly one-third of the population is zinc (Zn) deficient. Breeding healthier rice varieties is one of the major sustainable interventions to tackle micronutrient deficiencies. However, genotype and environment interactions (G × E) are a major obstacle in breeding for high-Zn rice varieties, thus an understanding of G × E interactions and identifying stable genotypes through multi-location evaluation will help in identifying potential lines for varietal release. We evaluated eight high-Zn rice breeding lines along with checks in several locations across the Philippines during 2014 wet season (WS), 2015 dry season (DS) and 2015WS, and 2016DS. Individual and combined analysis of variance revealed significant genotypic effects and G × E interactions for all the traits studied. Significant positive correlations between grain iron (Fe) and Zn, days to maturity, and plant height were observed, whereas grain yield and Zn were negatively correlated. Stability analysis using Kang’s stability index, additive main effects and multiplicative interaction, and genotype main effects plus G × E (GGE) consistently identified IR10M300 as the most stable genotype across seasons in terms of yield and grain Zn. Over all IR10M300 has a yield of 4690.3 kg ha−1 and grain Zn of 18.3 ppm. It outperformed two rice variety checks (PSBRc82 and MS13) for grain Zn with comparable yield with the yield check (PSBRc82) and was successfully released as the first High-Zinc Rice 1 (NSICRc 460) in the Philippines.

Analysis of genetic control and QTL mapping of essential wheat grain quality traits in a recombinant inbred population.

Abstract: Wheat cultivars are genetically crossed to improve end-use quality for traits as per demands of baking industry and broad consumer preferences. The processing and baking qualities of bread wheat are influenced by a variety of genetic make-ups, environmental factors and their interactions. Two wheat cultivars, WL711 and C306, derived recombinant inbred lines (RILs) with a population of 206, were used for phenotyping of quality-related traits. The genetic analysis of quality traits showed considerable variation for measurable quality traits, with normal distribution and transgressive segregation across the years. From the 206 RILs, few RILs were found to be superior to those of the parental cultivars for key quality traits, indicating their potential use for the improvement of end-use quality and suggesting the probability of finding new alleles and allelic combinations from the RIL population. Mapping analysis identified 38 putative QTLs for 13 quality-related traits, with QTLs explaining 7.9-16.8% phenotypic variation spanning over 14 chromosomes, i.e., 1A, 1B, 1D, 2A, 2D, 3B, 3D, 4A, 4B, 4D, 5D, 6A, 7A and 7B. In-silico analysis based on homology to the annotated wheat genes present in database, identified six putative candidate genes within QTL for total grain protein content, qGPC.1B.1 region. Major QTL regions for other quality traits such as TKW have been identified on 1B, 2A, and 7A chromosomes in the studied RIL population. This study revealed the importance of the combination of stable QTLs with region-specific QTLs for better phenotyping, and the QTLs presented in our study will be useful for the improvement of wheat grain and bread-making quality.

Genotype x environment interaction and genetic gain for grain yield and grain quality traits in Turkish spring wheat released between 1964 and 2010.

Abstract: The study was conducted to determine the effects of genotype (G), environment (E), their interaction (GEI) and genetic gain on yield and grain quality traits in Turkish spring wheat cultivars released between 1964 and 2010. We conducted a multi-environment trial at three testing locations: Adana, Adapazari, and Izmir, during the 2009, 2011 and 2013 cropping seasons and tested 35 cultivars released by the respective breeding programs. Allelic variations of high and low molecular weight glutenin subunits (HMW-GS and LMW-GS) and 1B/1R translocation was also determined and evaluated in all cultivars. Comparing yield across three locations, Adana (6416 kg ha-1) yield was relatively higher than in Izmir (5887 kg ha-1) and Adapazari (5205 kg ha-1) (P<0.001). Overall, GY was influenced by the varieties, testing location and breeding programs (P<0.001). Cultivars from Izmir breeding program performed relatively better (6174 kg ha-1) than those from Adana (5996 kg ha-1) and Adapazari (5351 kg ha-1) (<0.001). We recommend Ziyabey-98, Menemen, and Basribey-95, for stable grain yield in spring wheat production across the studied regions because of their wide adaptability, and Pamukova-97 for future breeding to improve grain quality parameters. We found three breeding programs have successfully increased the grain yield and quality traits for 46 years. As a group, cultivars released after 2000 had the highest yield indicating breeding progress. Genetic gain for GY was 30.9 kg ha-1 per year from 1964 with annual increase compared to the yield of older cultivar Akova B-2 (4102 kg ha-1) which constitutes a 0.75% rate of genetic gain. Improvement in grain quality was related to change in protein composition rather than an increase in protein content whereas yield improvement seems to mainly be related to increases in test weight and 1000 kernel weight. High molecular weight glutenin subunit (HMW-GS) 5+10 showed an increase in frequency whereas 2+12 showed a decrease over the breeding period.

Genome wide genetic dissection of wheat quality and yield related traits and their relationship with grain shape and size traits in an elite × non-adapted bread wheat cross.

Abstract: 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.

Hybridisation-based target enrichment of phenology genes to dissect the genetic basis of yield and adaptation in barley.

Abstract: Barley (Hordeum vulgare L.) is a major cereal grain widely used for livestock feed, brewing malts and human food. Grain yield is the most important breeding target for genetic improvement and largely depends on optimal timing of flowering. Little is known about the allelic diversity of genes that underlie flowering time in domesticated barley, the genetic changes that have occurred during breeding, and their impact on yield and adaptation. Here we report a comprehensive genomic assessment of a worldwide collection of 895 barley accessions based on the targeted resequencing of phenology genes. A versatile target‐capture method was used to detect genome‐wide polymorphisms in a panel of 174 flowering time‐related genes, chosen based on prior knowledge from barley, rice, and Arabidopsis thaliana. Association studies identified novel polymorphisms that accounted for observed phenotypic variation in phenology and grain yield, and explained improvements in adaptation as a result of historical breeding of Australian barley cultivars. We found that 50% of genetic variants associated with grain yield, and 67% of the plant height variation was also associated with phenology. The precise identification of favourable alleles provides a genomic basis to improve barley yield traits and to enhance adaptation for specific production areas.

Collection and Evaluation of Genetic Diversity and Population Structure of Potato Landraces and Varieties in China

Abstract: China is the world's leading country for potato production but potato is not native to China. To gain insights into the genetic diversity of potato germplasm various studies have been performed but no study has been reported for potato landraces in China. To improve the available genepool for future potato breeding programs, a diverse population containing 292 genotypes (including foreign elite lines, local landraces and cultivars) was developed and genotyped using 30 SSR markers covering the entire potato genome. A total of 174 alleles were detected with an average of 5.5 alleles per locus. The model-based structure analysis discriminated the population into two main sub-groups, which can be further subdivided into seven groups based on collection sites. One sub-group (P1) revealed less genetic diversity than other (P2) and contained a higher number of commercial cultivars possibly indicating a slight reduction in diversity due to selection in breeding programs. The P2 sub-group showed a wider range of genetic diversity with more new and unique alleles attained from wild relatives. The potato landraces, clustered in sub-population P1 may be derived from historical population imported from ancient European and International Potato Center genotypes while sub-population P2 may be derived from modern populations from International Potato Center and European genotypes. It is proposed that in the first step, the potato genotypes were introduced from Europe to China, domesticated as landraces, and then hybridized for modern cultivars.

Deciphering the genetic basis of root morphology, nutrient uptake, yield, and yield-related traits in rice under dry direct-seeded cultivation systems

Abstract: In the face of global water scarcity, a successful transition of rice cultivation from puddled to dry direct-seeded rice (DDSR) is a future need. A genome-wide association study was performed on a complex mapping population for 39 traits: 9 seedling-establishment traits, 14 root and nutrient-uptake traits, 5 plant morphological traits, 4 lodging resistance traits, and 7 yield and yield-contributing traits. A total of 10 significant marker-trait associations (MTAs) were found along with 25 QTLs associated with 25 traits. The percent phenotypic variance explained by SNPs ranged from 8% to 84%. Grain yield was found to be significantly and positively correlated with seedling-establishment traits, root morphological traits, nutrient uptake-related traits, and grain yield-contributing traits. The genomic colocation of different root morphological traits, nutrient uptake-related traits, and grain-yield-contributing traits further supports the role of root morphological traits in improving nutrient uptake and grain yield under DDSR. The QTLs/candidate genes underlying the significant MTAs were identified. The identified promising progenies carrying these QTLs may serve as potential donors to be exploited in genomics-assisted breeding programs for improving grain yield and adaptability under DDSR.

Rice, Marker-Assisted Breeding, and Disease Resistance

Abstract: In the last few decades, feeding the exponentially increasing human population has been always the biggest challenge for our plant breeders and scientists. To meet this, every plant breeder has focused on developing new and better crop varieties. Earlier, the characters selection was solely based on phenotypic observations, without the knowledge of molecular markers. However, marker-assisted breeding has emerged as the major efficient, sustainable, and accurate breeding approach employed in the last three decades. It has become breeder’s choice for introgression of genes into the recurrent parent for genetic improvement of traits including disease resistance, insect resistance, abiotic stress tolerance, taste improvement, aroma, mineral content, water use efficiency, and overall yield. This approach is highly promising as it allows pyramiding of target trait(s) in a single progeny in a very precise, stable, convenient, and fast manner. As a result, various quantitative trait loci (QTLs) and genes tightly linked to DNA markers governing resistance to rice blast disease, bacterial blight of rice, and other diseases have been identified, mapped, and transferred into susceptible lines, varieties, cultivars, and landraces of various crops including rice (Oryza sativa L.) worldwide. Overall, this book chapter reviews the use of marker-assisted breeding (MAB) for disease resistance in rice.

QTL analysis and candidate gene identification for plant height in cotton based on an interspecific backcross inbred line population of Gossypium hirsutum × Gossypium barbadense.

Abstract: We constructed the first high-quality and high-density genetic linkage map for an interspecific BIL population in cotton by specific-locus amplified fragment sequencing for QTL mapping. A novel gene GhPIN3 for plant height was identified in cotton. Ideal plant height (PH) is important for improving lint yield and mechanized harvesting in cotton. Most published genetic studies on cotton have focused on fibre yield and quality traits rather than PH. To facilitate the understanding of the genetic basis in PH, an interspecific backcross inbred line (BIL) population of 250 lines derived from upland cotton (Gossypium hirsutum L.) CRI36 and Egyptian cotton (G. barbadense L.) Hai7124 was used to construct a high-density genetic linkage map for quantitative trait locus (QTL) mapping. The high-density genetic map harboured 7,709 genotyping-by-sequencing (GBS)-based single nucleotide polymorphism (SNP) markers that covered 3,433.24 cM with a mean marker interval of 0.67 cM. In total, ten PH QTLs were identified and each explained 4.27–14.92% of the phenotypic variation, four of which were stable as they were mapped in at least two tests or based on best linear unbiased prediction in seven field tests. Based on functional annotation of orthologues in Arabidopsis and transcriptome data for the genes within the stable QTL regions, GhPIN3 encoding for the hormone auxin efflux carrier protein was identified as a candidate gene located in the stable QTL qPH-Dt1-1 region. A qRT-PCR analysis showed that the expression level of GhPIN3 in apical tissues was significantly higher in four short-statured cotton genotypes than that in four tall-statured cotton genotypes. Virus-induced gene silencing cotton has significantly increased PH when the expression of the GhPIN3 gene was suppressed.

Genetic Variability and Correlation Coefficients of Major Traits in Early Maturing Rice under Rainfed Lowland Environments of Nepal

Abstract: Genetic variability is the fundamental requirement of any crop breeding program to develop superior cultivars. The objective of this study was to estimate the genetic variability and find out the correlation among the different quantitative traits of rainfed early lowland rice. The experiment was conducted consecutively two years during 2015 and 2016 in wet season across the four different locations in Regional Agricultural Research Station, Khajura, National Wheat Research Program, Bhairahawa, National Maize Research Program, Rampur, and National Rice Research Program, Hardinath, along the Terai region of Nepal representing subtropical agroclimate. Seven genotypes including Hardinath-1 as standard check variety were evaluated in the randomized complete block design with three replications. Various quantitative traits were measured to investigate the variability and correlation coefficients. All the genotypes and locations showed significant variations for all the traits considered. Genotypic coefficient of variation was lower than phenotypic coefficient of variation for all traits studied. The magnitudes of genotypic coefficient of variations were relatively higher for grain yield, 1000-grain weight, and days to heading. The highest broad sense heritability of 94% was recorded in days to maturity and the lowest heritability of 16% was observed in plant height. Positive and highly significant correlations were found both in genotypic and phenotypic levels between days to heading and days to maturity (rg=0.9999 , rp=0.997 ), days to heading and grain yield (rg =0.9999 , rp= 0.9276 ), and days to maturity and grain yield (rg =0.9796 , rp=0.9174 ). However, negative and highly significant genetic correlation was observed between plant height and 1000-grain weight (rg = -0.9999 ). Thus results indicated that days to heading, days to maturity, grain yield, 1000-grain weight demonstrating higher heritability and remarkable genetic advance could be considered the most appropriate traits for improvement and selection of trait to achieve stable and high yielding early rice genotypes under rainfed environments.

QTLian breeding for climate resilience in cereals: progress and prospects.

Abstract: The ever-rising population of the twenty-first century together with the prevailing challenges, such as deteriorating quality of arable land and water, has placed a big challenge for plant breeders to satisfy human needs for food under erratic weather patterns. Rice, wheat, and maize are the major staple crops consumed globally. Drought, waterlogging, heat, salinity, and mineral toxicity are the key abiotic stresses drastically affecting crop yield. Conventional plant breeding approaches towards abiotic stress tolerance have gained success to limited extent, due to the complex (multigenic) nature of these stresses. Progress in breeding climate-resilient crop plants has gained momentum in the last decade, due to improved understanding of the physiochemical and molecular basis of various stresses. A good number of genes have been characterized for adaptation to various stresses. In the era of novel molecular markers, mapping of QTLs has emerged as viable solution for breeding crops tolerant to abiotic stresses. Therefore, molecular breeding-based development and deployment of high-yielding climate-resilient crop cultivars together with climate-smart agricultural practices can pave the path to enhanced crop yields for smallholder farmers in areas vulnerable to the climate change. Advances in fine mapping and expression studies integrated with cheaper prices offer new avenues for the plant breeders engaged in climate-resilient plant breeding, and thereby, hope persists to ensure food security in the era of climate change.

Heterosis and combining ability in cytoplasmic male sterile and doubled haploid based Brassica oleracea progenies and prediction of heterosis using microsatellites

Abstract: In Brassica oleracea, heterosis is the most efficient tool providing impetus to hybrid vegetable industry. In this context, we presented the first report on identifying superior heterotic crosses for yield and commercial traits in cauliflower involving cytoplasmic male sterile (CMS) and doubled haploid (DH) lines as parents. We studied the suitability of genomic-SSRs and EST-SSRs based genetic distance (GD) and agronomic trait based phenotypic distance (PD) for predicting heterosis in F1 hybrids using CMS and DH based parents. 120 F1 hybrids derived from 20Ogura based CMS lines and 6 DH based testers were evaluated for 16 agronomic traits along with the 26 parental lines and 4 commercial standard checks. The genomic-SSRs and EST-SSRs based genetic structure analysis grouped the 26 parental lines into 4 distinct clusters. The CMS lines Ogu118-6A, Ogu33A, Ogu34-1A were good general combiner for developing early maturity hybrids. The SCA effects were significantly associated with heterosis suggesting non-additive gene effects for the heterotic response of hybrids. Less than unity value of σ2A/D coupled with σ2gca/σ2sca indicated the predominance of non-additive gene action in the expression of studied traits. The correlation analysis of genetic distance with heterosis for commercial traits suggested that microsatellites based genetic distance estimates can be helpful in heterosis prediction to some extent.

Soybean genetic progress in South Brazil: physiological, phenological and agronomic traits

Abstract: Yield increase in soybean [Glycine max (L.) Merr.] has occurred due to plant breeding, as well as the improvement in management practices. Genetic gain for important traits in soybean due to plant breeding in South Brazil has not been evaluated. The objective of this study was to measure the genetic progress of several soybean agronomic, phenological and physiological traits, in a historical set of cultivars released for cultivation in South Brazil from 1965 to 2011. Twenty-nine cultivars were evaluated in a three replicate randomized complete block design at two locations in the 2016/17 crop season. Mean genetic gain for yield was 40.06 kg ha−1 year−1 averaged across locations. The modern cultivars had higher biological yield (BY), harvest index (HI), number of pods per plant (NPP), and lower number of branches per plant, plant height, and lodging score compared to older releases. There was a reduction in the vegetative period, and increase in ratio between reproductive and vegetative periods (R/V). Photosynthetic rate (PN) and transpiration rate (Tr) also increased with year of release. The traits BY, NPP, HI, R/V, number of seeds per pod, PN, Tr, and chlorophyll content (Chl a and b) was highly associated with seed yield. Breeding strategies that maximize the R/V ratio, and prioritize indirect selection through HI, BY, NPP, PN, Tr, and Chl a and b, will likely contribute to improving soybean yield in the future.

Assessment of agro-morphological variability of dry-season sorghum cultivars in Chad as novel sources of drought tolerance.

Abstract: Dry-season sorghum is a type of sorghum whose establishment ends at the end of the rainy season and its development takes place during the dry and cold harmattan period. Its root system is particularly well developed with deep penetration for water withdrawal. This study was conducted to assess the level of genetic diversity present among dry-season sorghum in Chad’s Sudanese zone using phenotypic traits, and to identify new sources of drought tolerance that could be used in sorghum breeding programs. A high variability in qualitative traits was observed except for the botanical race which showed that all cultivars were of durra race. It was also observed that most cultivars had compact panicles (66.67%), mostly black glumes (66.67%), glume hairiness (58.33%) and did not have aristation (91.67%). Most qualitative traits showed a coefficient of variation of less than 30%, and the analysis of the variance showed that at 0.1% probability, there were significant differences between cultivars for all traits except botanical race. It was observed that the potential productivity of dry-season sorghum of this collection was strongly related to their staygreen characteristic; a trait of enormous importance in breeding for postflowering drought tolerance in sorghum. Plant height was highly heritable (91.9%), followed by the peduncle length (90.2%), panicle length (87.5%) and the internodes number (86.5%). Structuring of diversity separated the cultivars into four statistically distinct groups; with group 2 clustering cultivars with panicle productivity, early maturity and high staygreen, and other traits that contribute to the performance of cultivars. The findings will help to enhance the selection and production of dry-season sorghum in Chad and also provide alternative sources for staygreen introgression into the larger sorghum breeding community.

Genome-wide variation patterns between landraces and cultivars uncover divergent selection during modern wheat breeding.

Abstract: Genetic diversity, population structure, LD decay, and selective sweeps in 687 wheat accessions were analyzed, providing relevant guidelines to facilitate the use of the germplasm in wheat breeding. Common wheat (Triticum aestivum L.) is one of the most widely grown crops in the world. Landraces were subjected to strong human-mediated selection in developing high-yielding, good quality, and widely adapted cultivars. To investigate the genome-wide patterns of allelic variation, population structure and patterns of selective sweeps during modern wheat breeding, we tested 687 wheat accessions, including landraces (148) and cultivars (539) mainly from China and Pakistan in a wheat 90 K single nucleotide polymorphism array. Population structure analysis revealed that cultivars and landraces from China and Pakistan comprised three relatively independent genetic clusters. Cultivars displayed lower nucleotide diversity and a wider average LD decay across whole genome, indicating allelic erosion and a diversity bottleneck due to the modern breeding. Analysis of genetic differentiation between landraces and cultivars from China and Pakistan identified allelic variants subjected to selection during modern breeding. In total, 477 unique genome regions showed signatures of selection, where 109 were identified in both China and Pakistan germplasm. The majority of genomic regions were located in the B genome (225), followed by the A genome (175), and only 77 regions were located in the D genome. EigenGWAS was further used to identify key selection loci in modern wheat cultivars from China and Pakistan by comparing with global winter wheat and spring wheat diversity panels, respectively. A few known functional genes or loci found within these genome regions corresponded to known phenotypes for disease resistance, vernalization, quality, adaptability and yield-related traits. This study uncovered molecular footprints of modern wheat breeding and explained the genetic basis of polygenic adaptation in wheat. The results will be useful for understanding targets of modern wheat breeding, and in devising future breeding strategies to target beneficial alleles currently not pursued.

Genetic dissection of agronomic and quality traits based on association mapping and genomic selection approaches in durum wheat grown in Southern Spain.

Abstract: Climatic conditions affect the growth, development and final crop production. As wheat is of paramount importance as a staple crop in the human diet, there is a growing need to study its abiotic stress adaptation through the performance of key breeding traits. New and complementary approaches, such as genome-wide association studies (GWAS) and genomic selection (GS), are used for the dissection of different agronomic traits. The present study focused on the dissection of agronomic and quality traits of interest (initial agronomic score, yield, gluten index, sedimentation index, specific weight, whole grain protein and yellow colour) assessed in a panel of 179 durum wheat lines (Triticum durum Desf.), grown under rainfed conditions in different Mediterranean environments in Southern Spain (Andalusia). The findings show a total of 37 marker-trait associations (MTAs) which affect phenotype expression for three quality traits (specific weight, gluten and sedimentation indexes). MTAs could be mapped on the A and B durum wheat subgenomes (on chromosomes 1A, 1B, 2A, 2B and 3A) through the recently available bread wheat reference assembly (IWGSC RefSeqv1). Two of the MTAs found for quality traits (gluten index and SDS) corresponded to the known Glu-B1 and Glu-A1 loci, for which candidate genes corresponding to high molecular weight glutenin subunits could be located. The GS prediction ability values obtained from the breeding materials analyzed showed promising results for traits as grain protein content, sedimentation and gluten indexes, which can be used in plant breeding programs.

Multi-Parental Advances Generation Inter-Cross Population, to Develop Organic Tomato Genotypes by Participatory Plant Breeding

Abstract: A Multi-parent Advanced Generation Intercross (MAGIC) tomato population was developed by crossing eight founder lines chosen to include a wide range of variability. The lines were previously genotyped by a genotyping by sequencing approach. The MAGIC population was used to develop genotypes with important agronomic traits and to perform the Participatory Plant Breeding (PPB). Among the 400 plants of generation 4 (G4) of the MAGIC population cultivated in an organic field experiment, 22 individuals were phenotypically selected and a molecular analysis was done for both presence of resistance genes and fruit shape (marker assisted selection) on G5 seedlings. Three selected plants showed both the pyramiding gene of resistance to the main diseases and the ovate gene for pear shape typology. The 400 G10 stable lines that obtained from single seed descent will represent an important genetic resource for the tomato scientific community. The MAGIC population G4 was also cultivated in three organic farms located in North, Central and South Italy to carry out the PPB. The plants showed significant phenotypic differences in development, productivity and fruit color. This variability was used to select families of tomato adapted to low input crop management, different environments, agricultural practices and market conditions.

Recent Advances in Wheat (Triticum spp.) Breeding

Abstract: Wheat (Triticum spp. L; Gramineae), a self-pollinating crop, is one of the most important cereal crops. Globally, wheat is an economic crop, utilized as food, feed, seed and industrial uses. Gene banks have conserved a large genetic resource collection of wheat germplasm including wild Triticum species. There are numerous species of Triticum with different genomes and chromosome numbers. Triticum harbors significant diversity based on ploidy level, biological status, geographical regions and morpho-agronomic traits. Introgression of novel alleles through crossing between various wheat genetic resources, e.g. modern varieties with locally-adapted varieties, enhances genetic diversity and preselection for traits of interest, which is required to ensure meaningful natural variation at the phenotype level. Improving wheat for biotic and abiotic stress tolerance traits, quality traits and yield attributes are the main objectives of wheat breeders and geneticists. Achieving these objectives can be facilitated by the application the modern genomics tools to augment traditional breeding programs. This chapter presents an overview of wheat germplasm biodiversity and conservation, objectives and stages of wheat breeding programs, cultivation and traditional breeding methods, in addition to modern plant breeding tools including marker-assisted breeding, genetic engineering and genome editing.

Doubled Haploidy Techniques in Wheat (Triticum aestivum L.): An Overview

Abstract: Wheat crop has a critical role in current food system and also in the future global food security. Global wheat demand in 2010 reached 666 million metric tons (MMT). If the demand growth rate remains constant, it has been predicted that the global wheat consumption would surpass 880 MMT by 2050. Fulfilling this demand needs new and more efficient wheat breeding methodologies. Conventional breeding has led to the development of number of varieties, but with the changing climatic regime accompanied with fast and continuous changing nature of biotic and abiotic stresses there is an urgent need to fasten the breeding methods. Hence, biotechnological tool like DH becomes an important weapon. The production of haploid plants from hybrids, followed by chromosome doubling will provide wheat breeder with a mean to accelerate the development of true breeding lines. Doubled haploid (DH) populations have lot of applications in plant breeding like cultivar and germplasm development, transferring traits from wild types, studying components of quantitative genetics and whole genome mapping. Among different DH production techniques, anther culture and Hordeum bulbosum have stronger genotypic specificity whereby, wide hybridization comes up with a solution. Amongst various wide hybridization techniques, DH production via Imperata cylindrica has been found to be the most economical and efficient. The genotypic nonspecific production lacks somaclonal variation and albino plants development alongwith having higher regeneration rate coupled with lower cost. Thus, integration of I. cylindrica mediated DH system with conventional breeding will be instrumental for future wheat breeding programmes.

Towards high-biomass yielding bioenergy crop Silphium perfoliatum L.: phenotypic and genotypic evaluation of five cultivated populations

Abstract: Cup plant (Silphium perfoliatum L.) represents a promising alternative to silage maize as an energy crop for biogas production. This non-food plant possesses a highly ecological value due to its long blooming period, ability to grow in low-input agriculture and positive influence on soil structure. So far, there have been almost no breeding attempts for the cup plant, and all field experiments showing its high biomass yield were conducted by using only a few cultivated populations of unclear ancestry. Comprehensive assessment of five such populations for their biomass and methane yield parameters revealed substantial genetic variations indicating the possibility of improving these traits through selection and breeding. Higher biomass yield is likely to be achieved by breeding for secondary traits such as plant height, shoot diameter and internode number as well as photoperiod response. For increasing the methane production, reduced lignin or fibre content in the biomass seems to be important. Genetic relationships among the populations were estimated using tunable genotyping by sequencing (tGBS) technology. Genetic structure and phylogeny analyses revealed that all the plants belong to the same gene pool and share a common ancestry. Four out of five populations demonstrate a low genetic differentiation, whereas the fifth one represents a clear example of population stratification. To achieve a successful domestication and breeding of this new high-yielding perennial crop, a broader base of genetic diversity needs to be ensured and complemented by innovative breeding strategies driven by molecular genetic and modern genomics approaches.