Rapid Generation Advance in Chickpea for Accelerated Breeding Gain in Ethiopia: : What Speed Breeding Imply?

አህፅሮት  ሽምብራ በሀገራችን በተለያዩ ስነ-ምህዳራትና የአዘማመር ስርዓት ውስጥ የሚመረት ሰብል ነው፡፡ የሰብሉ የመድረሻ ተለያይነት በዓለም ላይ ከ80 አስከ 180 ቀናት ይደርሳል፡፡ እያደገ ያለውን ህዝብና የተለያዩ ፍላጎቶችን ለመመለስ የሰብል ማሻሻያ ስርዓቱ ጊዜን በቆጠበ ሁኔታ መከወን የሚያስችሉ ዘዴዎችን መጠቀሙ አንዱ የችግሩ መፍቻ መንገድ ነው፡፡ በዚህ ጥናት ላይ የሰብሉን ማሻሻያ ለማፍጠን እንዴት በርካታ ትውልዶቸን በአንድ ዓመት ማግኘት እንደሚቻል ቀርቧል፡፡ አስር የሚሆኑ ምርት ላይ ያሉ የሽምብራ ዝርያዎችን ከሌሎች ዘጠኝ በዘመናዊ ላብራቶሪ ልየታ ድርቅን የሚቋቋም ባህሪ ያላቸውን ቤተሰቦቸ በማዳቀል ሂደት ወደ 46 ግንኙነቶችን መፍጠር የተቻለበትንና ትውልዶችን ማፍጠንንና ማግኘትን በትኩረት ተከናውኗል፡፡ ዓላማውም ድርቅን የሚቋቋሙና ምርታማ ትውልዶችን ፍተሻ ማድረግ ሲሆን ይህንንም ባጭር ጊዜ ውስጥ ለመከወን አዲስ የነጠላ ዘር ትውልድ ማሻገሪያ ስርዓትን ከቀድሞ ደራሽ እምቡጦች ጋር በማቀናጀት አራት ትውልዶችን በዓመት ማግኘት የተቻለበትን ሁኔታ ማረጋገጥ ተችሏል፡፡ ይህ ትውልዶችን የማስኬድ ሁኔታ በአንድ አመት ጊዜ ውስጥ በወረርና የደብረዘይት ማእከላት የሙከራ ማሳዎችን በመጠቀም የተሰራ ጥናት ሲሆን በውጤቱም ቀድሞ ደራሽ እምቡጦችን ለማግኘት ከ80-85 ቀናት ብቻ የፈጀ ነበር፡፡ ትውልዶቹ የመካከለኛ መድረሻ ጊዜ ያለው ውስጥ የሚመደቡ ሲሆን በዚህ ስሌት የዝርያ መልቀቂያ ጊዜውን ከተለመደው 10-12 ዓመታት 50 በመቶ በመቀነስ የአማራጭ ቴክኖሎጂ አቅርቦትና ምርታማነት እንዲሁም አዋጭነት ላይ ከፍተኛ አስተዋፅዖ ያለው ውጤት አመላክቷል፡፡ ይህ ቴክኒክ በቶሎ የመድረሻ ዕድሜ ያላቸው ላይ ተፅዕኖው አስከ ስድስት ትውልድ በዓመት ማስገኘት እንደሚያስችል የተሰላ ሲሆን በቀላሉ የሚለመድ፣ በጥቂት የመዋዕለ ነዋይ፣ ፋሲሊቲና ክህሎት በትሮፒካል ንፍቀ-ክበብ ውስጥ አገልግሎት ላይ ሊውል የሚችልና ቴክኖሎጂ ለቀቃን ብሎም መተካካትን የሚያፋጥን፤ በዚህም ረገድ የምርታማነት እመርታን የሚያስገኝ የተሻሻለ ዘዴ እንደሆነ መገንዘብ ተችሏል፡፡ Abstract Chickpea (Cicer arietinum L.) is grown in a wide range of environments and cropping systems and its maturity ranges from 80 to 180 days. Time-saving breeding is key to responding to the dynamics of demands and environmental changes. The study employed the Single Seed Descent (SSD) technique in advancing the generation, supported by the independent observation of chickpea seed germination and seedling establishment in the seed lab. The filial generation nursery was derived from 46 initial crosses with the aim of enhancing drought and yield response of otherwise commercial 10 cultivars. Between 5 December 2017 and 20 December 2018 we were able to obtain four rounds of working chickpea seeds (F2-F5) using two research locations. The average time required to obtain early matured pods varied from 80 to 85 days. Harvesting four generations in an annual cycle enables a saving of at least 50% time in variety release, which has the potential to double the rate of genetic gain and variety replacement. As long as measures are taken to reduce risk associated with extreme weather events or animal damage, this low-cost rapid cycling approach could be adapted for large-scale breeding programs to fast track the development of more productive varieties

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. On the basis of WGS of 3,366 chickpea germplasm accessions, we report here a rich map of the genetic variation in chickpea. We provide a chickpea pan-genome and offer insights into species divergence, the migration of the cultigen (C. arietinum), rare allele burden and fitness loss in chickpea. We propose three genomic breeding approaches— haplotype-based breeding, genomic prediction and OCS—for developing tailor-made high-yielding and climate-resilient chickpea varieties. We sequenced 3,366 chickpea germplasm lines, including 3,171 cultivated and 195 wild accessions at an average coverage of around 12× (Methods, Extended Data Fig. 1, Supplementary Data 1 Tables 1, 2). Alignment of WGS data to the CDC Frontier reference genome11 identified 3.94 million and 19.57 million single-nucleotide polymorphisms (SNPs) in 3,171 cultivated and 195 wild accessions, respectively (Extended Data Table 1, Supplementary Data 1 Tables 3–7, Supplementary Notes). This SNP dataset was used to assess linkage disequilibrium (LD) decay (Supplementary Data 2 Tables 1, 2, Extended Data Fig. 2, Supplementary Notes) and identify private and population-enriched SNPs (Supplementary Data 3 Tables 1–4, Supplementary Notes). These private and population-enriched SNPs suggest rapid adaptation and can enhance the genetic foundation in the elite gene pool

Resistance to plant-parasitic nematodes in chickpea: current status and future perspectives

Plant-parasitic nematodes constrain chickpea (Cicer arietinum) production, with annual yield losses estimated to be 14% of total global production. Nematode species causing significant economic damage in chickpea include root-knot nematodes (Meloidogyne artiella, M. incognita, M. javanica), cyst nematode (Heterodera ciceri), and root-lesion nematode (Pratylenchus thornei). Reduced functionality of roots from nematode infestation leads to water stress and nutrient deficiency, which in turn lead to poor plant growth and reduced yield. Integration of resistant crops with appropriate agronomic practices is recognized as the safest and most practical, economic and effective control strategy for plant-parasitic nematodes. However, breeding for resistance to plant-parasitic nematodes has numerous challenges that originate from the narrow genetic diversity of the C. arietinum cultigen. While levels of resistance to M. artiella, H. ciceri and P. thornei have been identified in wild Cicer species that are superior to resistance levels in the C. arietinum cultigen, barriers to interspecific hybridization restrict the use of these crop wild relatives, as sources of nematode resistance. Wild Cicer species of the primary genepool, C. reticulatum and C. echinospermum, are the only species that have been used to introgress resistance genes into the C. arietinum cultigen. The availability of genomic resources, including genome sequence and re-sequence information, the chickpea reference set and mini-core collections, and new wild Cicer collections, provide unprecedented opportunities for chickpea improvement. This review surveys progress in the identification of novel genetic sources of nematode resistance in international germplasm collections and recommends genome-assisted breeding strategies to accelerate introgression of nematode resistance into elite chickpea cultivars

CicArVarDB: SNP and InDel database for advancing genetics research and breeding applications in chickpea

Molecular markers are valuable tools for breeders to help accelerate crop improvement. High throughput sequencing technologies facilitate the discovery of large-scale variations such as single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs). Sequencing of chickpea genome along with re-sequencing of several chickpea lines has enabled the discovery of 4.4 million variations including SNPs and InDels. Here we report a repository of 1.9 million variations (SNPs and InDels) anchored on eight pseudomolecules in a custom database, referred as CicArVarDB that can be accessed at http://cicarvardb.icrisat.org/. It includes an easy interface for users to select variations around specific regions associated with quantitative trait loci, with embedded webBLAST search and JBrowse visualisation. We hope that this database will be immensely useful for the chickpea research community for both advancing genetics research as well as breeding applications for crop improvement

Whole genome resequencing and phenotyping of MAGIC population for high resolution mapping of drought tolerance in chickpea

Terminal drought is one of the major constraints to crop production in chickpea (Cicer arietinum L.). In order to map drought tolerance related traits at high resolution, we sequenced multi-parent advanced generation intercross (MAGIC) population using whole genome resequencing approach and phenotyped it under drought stress environments for two consecutive years (2013-14 and 2014-15). A total of 52.02 billion clean reads containing 4.67 TB clean data were generated on the 1136 MAGIC lines and eight parental lines. Alignment of clean data on to the reference genome enabled identification of a total, 932,172 of SNPs, 35,973 insertions, and 35,726 deletions among the parental lines. A high-density genetic map was constructed using 57,180 SNPs spanning a map distance of 1606.69 cM. Using compressed mixed linear model, genome-wide association study (GWAS) enabled us to identify 737 markers significantly associated with days to 50% flowering, days to maturity, plant height, 100 seed weight, biomass, and harvest index. In addition to the GWAS approach, an identity-by-descent (IBD)-based mixed model approach was used to map quantitative trait loci (QTLs). The IBD-based mixed model approach detected major QTLs that were comparable to those from the GWAS analysis as well as some exclusive QTLs with smaller effects. The candidate genes like FRIGIDA and CaTIFY4b can be used for enhancing drought tolerance in chickpea. The genomic resources, genetic map, marker-trait associations, and QTLs identified in the study are valuable resources for the chickpea community for developing climate resilient chickpeas

Novel SSR Markers from BAC-End Sequences, DArT Arrays and a Comprehensive Genetic Map with 1,291 Marker Loci for Chickpea (Cicer arietinum L.)

Chickpea (Cicer arietinum L.) is the third most important cool season food legume, cultivated in arid and semi-arid regions of the world. The goal of this study was to develop novel molecular markers such as microsatellite or simple sequence repeat (SSR) markers from bacterial artificial chromosome (BAC)-end sequences (BESs) and diversity arrays technology (DArT) markers, and to construct a high-density genetic map based on recombinant inbred line (RIL) population ICC 4958 (C. arietinum)×PI 489777 (C. reticulatum). A BAC-library comprising 55,680 clones was constructed and 46,270 BESs were generated. Mining of these BESs provided 6,845 SSRs, and primer pairs were designed for 1,344 SSRs. In parallel, DArT arrays with ca. 15,000 clones were developed, and 5,397 clones were found polymorphic among 94 genotypes tested. Screening of newly developed BES-SSR markers and DArT arrays on the parental genotypes of the RIL mapping population showed polymorphism with 253 BES-SSR markers and 675 DArT markers. Segregation data obtained for these polymorphic markers and 494 markers data compiled from published reports or collaborators were used for constructing the genetic map. As a result, a comprehensive genetic map comprising 1,291 markers on eight linkage groups (LGs) spanning a total of 845.56 cM distance was developed (http://cmap.icrisat.ac.in/cmap/sm/cp/thudi/). The number of markers per linkage group ranged from 68 (LG 8) to 218 (LG 3) with an average inter-marker distance of 0.65 cM. While the developed resource of molecular markers will be useful for genetic diversity, genetic mapping and molecular breeding applications, the comprehensive genetic map with integrated BES-SSR markers will facilitate its anchoring to the physical map (under construction) to accelerate map-based cloning of genes in chickpea and comparative genome evolution studies in legumes

Genomic resources in plant breeding for sustainable agriculture

Climate change during the last 40 years has had a serious impact on agriculture and threatens global food and nutritional security. From over half a million plant species, cereals and legumes are the most important for food and nutritional security. Although systematic plant breeding has a relatively short history, conventional breeding coupled with advances in technology and crop management strategies has increased crop yields by 56 % globally between 1965-85, referred to as the Green Revolution. Nevertheless, increased demand for food, feed, fiber, and fuel necessitates the need to break existing yield barriers in many crop plants. In the first decade of the 21st century we witnessed rapid discovery, transformative technological development and declining costs of genomics technologies. In the second decade, the field turned towards making sense of the vast amount of genomic information and subsequently moved towards accurately predicting gene-to-phenotype associations and tailoring plants for climate resilience and global food security. In this review we focus on genomic resources, genome and germplasm sequencing, sequencing-based trait mapping, and genomics-assisted breeding approaches aimed at developing biotic stress resistant, abiotic stress tolerant and high nutrition varieties in six major cereals (rice, maize, wheat, barley, sorghum and pearl millet), and six major legumes (soybean, groundnut, cowpea, common bean, chickpea and pigeonpea). We further provide a perspective and way forward to use genomic breeding approaches including marker-assisted selection, marker-assisted backcrossing, haplotype based breeding and genomic prediction approaches coupled with machine learning and artificial intelligence, to speed breeding approaches. The overall goal is to accelerate genetic gains and deliver climate resilient and high nutrition crop varieties for sustainable agriculture

Integrated physical, genetic and genome map of chickpea (Cicer arietinum L.)

Physical map of chickpea was developed for the reference chickpea genotype (ICC 4958) using bacterial artificial chromosome (BAC) libraries targeting 71,094 clones (~12× coverage). High information content fingerprinting (HICF) of these clones gave high-quality fingerprinting data for 67,483 clones, and 1,174 contigs comprising 46,112 clones and 3,256 singletons were defined. In brief, 574 Mb genome size was assembled in 1,174 contigs with an average of 0.49 Mb per contig and 3,256 singletons represent 407 Mb genome. The physical map was linked with two genetic maps with the help of 245 BAC-end sequence (BES)-derived simple sequence repeat (SSR) markers. This allowed locating some of the BACs in the vicinity of some important quantitative trait loci (QTLs) for drought tolerance and reistance to Fusarium wilt and Ascochyta blight. In addition, fingerprinted contig (FPC) assembly was also integrated with the draft genome sequence of chickpea. As a result, ~965 BACs including 163 minimum tilling path (MTP) clones could be mapped on eight pseudo-molecules of chickpea forming 491 hypothetical contigs representing 54,013,992 bp (~54 Mb) of the draft genome. Comprehensive analysis of markers in abiotic and biotic stress tolerance QTL regions led to identification of 654, 306 and 23 genes in drought tolerance “QTL-hotspot” region, Ascochyta blight resistance QTL region and Fusarium wilt resistance QTL region, respectively. Integrated physical, genetic and genome map should provide a foundation for cloning and isolation of QTLs/genes for molecular dissection of traits as well as markers for molecular breeding for chickpea improvement