A chickpea genetic variation map based on the sequencing of 3,366 genomes

Zero hunger and good health could be realized by 2030 through effective conservation, characterization and utilization of germplasm resources1. So far, few chickpea (Cicerarietinum) germplasm accessions have been characterized at the genome sequence level2. Here we present a detailed map of variation in 3,171 cultivated and 195 wild accessions to provide publicly available resources for chickpea genomics research and breeding. We constructed a chickpea pan-genome to describe genomic diversity across cultivated chickpea and its wild progenitor accessions. A divergence tree using genes present in around 80% of individuals in one species allowed us to estimate the divergence of Cicer over the last 21 million years. Our analysis found chromosomal segments and genes that show signatures of selection during domestication, migration and improvement. The chromosomal locations of deleterious mutations responsible for limited genetic diversity and decreased fitness were identified in elite germplasm. We identified superior haplotypes for improvement-related traits in landraces that can be introgressed into elite breeding lines through haplotype-based breeding, and found targets for purging deleterious alleles through genomics-assisted breeding and/or gene editing. Finally, we propose three crop breeding strategies based on genomic prediction to enhance crop productivity for 16 traits while avoiding the erosion of genetic diversity through optimal contribution selection (OCS)-based pre-breeding. The predicted performance for 100-seed weight, an important yield-related trait, increased by up to 23% and 12% with OCS- and haplotype-based genomic approaches, respectively.

Hybrid Rice Outperforms Inbred Rice in Resistance to Sheath Blight and Narrow Brown Leaf Spot

Sheath blight (ShB, caused by Rhizoctonia solani AG1-1A) and narrow brown leaf spot (NBLS, Cercospora janseana) are among the most important diseases affecting rice production in Texas and other southern United States. Because of high yielding potential, hybrid rice acreage has continually increased. Understanding the relative levels of resistance to ShB and NBLS in hybrids over inbreds is important to effective disease management but remain largely unknown. Comparative performance of hybrid rice and inbred rice was evaluated with 173 hybrid and 155 inbred genotypes (cultivars and elite breeding lines) over five crop seasons (2016 to 2020) and two locations in Texas. The results show that genotype, cultivar type (hybrid or inbred), location, and their interactions had a significant effect on the severity of ShB and NBLS. ShB severities in hybrid genotypes were significantly lower than in inbred genotypes, with an average of 27% reduction in disease severity over the 5 year x 2 location evaluation. Most (53%) of the hybrid genotypes were rated moderately resistant (MR), whereas almost all (97%) of the inbred genotypes ranged from very susceptible (VS) to moderately susceptible (MS). Similarly, NBLS severities in hybrid genotypes are significantly lower than those in inbred genotypes. All but four hybrid genotypes exhibit immune reaction to NBLS. In contrast, 77% of the inbred genotypes exhibit the NBLS symptoms, with disease resistance reactions ranging from susceptible (S) to resistant (R). The results demonstrate that hybrid rice is generally less susceptible to sheath blight and has a higher level of resistance against NBLS compared to inbred rice.

Assessment of diversity in tropical soybean (Glycine max (L.) Merr.) varieties and elite breeding lines using single nucleotide polymorphism markers

Soybean (Glycine max (L.) Merr.) is an important legume crop with high commercial value widely cultivated globally. Thus, the genetic characterization of the existing soybean germplasm will provide useful information for enhanced conservation, improvement and future utilization. This study aimed to assess the extent of genetic diversity of soybean elite breeding lines and varieties developed by the soybean breeding programme of the International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria. The genetic diversity of 65 soybean genotypes was studied using single-nucleotide polymorphism (SNP) markers. The result revealed that 2446 alleles were detected, and the indicators for allelic richness and diversity had good differentiating power in assessing the diversity of the genotypes. The three complementary approaches used in the study grouped the germplasm into three major clusters based on genetic relatedness. The analysis of molecular variance revealed that 71% (P < 0.001) variation was due to among individual genotypes, while 11% (P < 0.001) was ascribed to differences among the three clusters, and the fixation index (FST) was 0.11 for the SNP loci, signifying moderate genetic differentiation among the genotypes. The identified private alleles indicate that the soybean germplasm contains diverse variability that is yet to be exploited. The SNP markers revealed high diversity in the studied germplasm and found to be efficient for assessing genetic diversity in the crop. These results provide valuable information that might be utilized for assessing the genetic variability of soybean and other legume crops germplasm by breeding programmes.

Diversity and genetic parameter of chili pepper (Capsicum annuum) based on yield component in three location

Sayekti TWDA, Syukur M, Hidayat SH, Maharijaya A. 2021. Diversity and genetic parameter of chili pepper (Capsicum annuum) based on yield component in three locations. Biodiversitas 22: 823-829. With the increase in the use of chili, it is necessary to develop these commodities through plant breeding activities. Phenotypes are not only determined by genetics, but also by environmental factors and the GxE interactions, so all the factors need to be considered. The aims of this study were to evaluate the variability of ten elite breeding lines and three commercial varieties of chili pepper (Capsicum annuum L.) across three different environments. This experiment was conducted in three environments namely Bogor, Kolaka, and Palembang, from January until July 2019. Thirteen genotypes consisting of ten elite lines and three commercial chili pepper were used. This experiment was arranged in a randomized complete block design (RCBD) with three replications for each environment. To determine the effect of environment, Combined Analysis of Variance was carried out for all environments using PBSTAT-GE. The environment used in this experiment was lowland that varies between each other. The genotype with the fastest harvesting age relative in three environments was F7-145293-19-8-3-113-1. The highest number of fruits per plant was observed in genotype F9-160291-9-4-3-2-1-1-1 with 261 fruits per plant. The highest yield was observed in genotype F7-145174-9-7-1-5-3. From the clustering analysis, this population was grouped into five clusters. The heritability values for the 12 observed traits ranged between 22.68-69.97%, classified into high and moderate criteria.

Characterization of elite bread wheat (Triticum aestivum L.) germplasm for spot blotch Bipolaris sorokiniana (Sacc.) Shoemaker resistance

Genetic resources are of paramount importance for developing improved crop varieties, particularly for biotic and abiotic stress tolerance. Spot blotch (SB) is a destructive foliar disease of wheat prevalent in warm and humid regions of the world, especially in the eastern parts of South Asia. For the management of this disease, the most effective measure is the development of resistant cultivars. Thus, the present investigation was carried out to confirm SB resistance in 200 germplasm accessions based on phenotypic observations and molecular characterization. These elite breeding lines obtained from the International Centre for Maize and Wheat Improvement, Mexico, are developed deploying multiple parentages. These lines were screened for SB resistance in the field under artificially created epiphytotic conditions during 2014–15 and 2015–16 along with two susceptible checks (CIANO T79 and Sonalika) and two resistant checks (Chirya 3 and Francolin). Eighty-two out of 200 germplasm accessions were found resistant to SB and resistance in these lines was confirmed with a specific SSR marker Xgwm148. Three accessions, VORONA/CNO79, KAUZ*3//DOVE/BUC and JUP/BJY//URES/3/HD2206/HORK//BUC/BUL were observed possessing better resistance than the well-known SB-resistant genotype Chirya3. These newly identified resistant lines could be used by wheat breeders for developing SB-resistant wheat varieties.

Enhancing the Nutritional Quality of Major Food Crops Through Conventional and Genomics-Assisted Breeding

Nutritional stress is making over two billion world population malnourished. Either our commercially cultivated varieties of cereals, pulses, and oilseed crops are deficient in essential nutrients or the soils in which these crops grow are becoming devoid of minerals. Unfortunately, our major food crops are poor sources of micronutrients required for normal human growth. To overcome the problem of nutritional deficiency, greater emphasis should be laid on the identification of genes/quantitative trait loci (QTLs) pertaining to essential nutrients and their successful deployment in elite breeding lines through marker-assisted breeding. The manuscript deals with information on identified QTLs for protein content, vitamins, macronutrients, micro-nutrients, minerals, oil content, and essential amino acids in major food crops. These QTLs can be utilized in the development of nutrient-rich crop varieties. Genome editing technologies that can rapidly modify genomes in a precise way and will directly enrich the nutritional status of elite varieties could hold a bright future to address the challenge of malnutrition.

Molecular Genetics, Genomics, and Biotechnology in Crop Plant Breeding

A diverse set of molecular markers techniques have been developed over the last almost 40 years and used with success for breeding a number of major crops. These have been narrowed down to a few preferred DNA based marker types, and emphasis is now on adapting the technologies to a wide range of crop plants and trees. In this Special Issue, the strength of molecular breeding is revealed through research and review papers that use a combination of molecular markers with other classic breeding techniques to obtain quality improvement of the crop. The constant improvement and maintenance of quality by breeding is crucial and challenged by a changing climate and molecular markers can support the direct introgression of traits into elite breeding lines. All the papers in this Special Issue “Molecular genetics, Genomics, and Biotechnology in Crop Plant Breeding” have attracted significant attention, as can be witnessed by the graphs for each paper on the Journal’s homepage. It is the hope that it will encourage others to use these tools in developing an even wider range of crop plants and trees.

Using soybean pedigrees to identify genomic selection signatures associated with long-term breeding for cultivar improvement

Genetic hitchhiking methods used to uncover selection signatures related to traits of agronomic importance in crops have primarily been used at the level of domestication by comparing groups of wild germplasm to landraces or elite breeding lines. In this study, two groups of cultivars defined by an elite Canadian soybean cultivar, ‘OAC Bayfield’, were compared to identify selection signatures related to long-term breeding within a specific region. Cultivars were assigned to either a pre- or post-OAC Bayfield group. Of the 162 simple sequence repeat markers used to genotype members of the pedigree, 14 were fixed and 19 exhibited a selective signature. An in silico analysis compared the results in this study to quantitative trait loci (QTL) reported in SoyBase and showed that 18 out of the 19 markers with a selective signature were associated with at least one QTL. From the 80 QTL associated with the 18 markers, half were related to plant architecture, yield, or maturity. In addition, the number and type of QTL associated with the fixed versus selected loci differed, particularly for yield. Genomic regions exhibiting a selection signature may contain important loci that either need to be conserved for agronomic performance or be targeted for introgressive breeding and germplasm enrichment.