New challenges in breeding chickpea under changing climate

Climate change is a continuous natural process leading to evolution of diverse flora and fauna. The variability thus created during process of evolution followed by selection of most fit by nature itself forms primary base for crop improvement programs. However, the industrialization led climate change in the present era has been witnessed in form of abrupt rise or drop in temperature, erratic or uneven and untimely rainfall resulting in floods and drought situations. This is a cause of concern as such changes have direct impact on food production. Since most of the pulse crops including chickpea is sensitive to such climate changes, there is need to define likely effects of climate change on chickpea crop and strategies to mitigate its impact on chickpea production and productivity. Among various abiotic and biotic stresses likely to emerge are deficient or high soil moisture, frequent and untimely rains leading to unseasonal flood like situations during winter season, extreme temperatures during different crop growth stages such as frost during vegetative stage, low or high temperature at reproductive stage leading to flower/pod drop and abrupt rise in temperature during vegetative stage leading to initiation of early flowering followed by sudden drop in temperature leading to flower or pod drop; excessive crop growth due to frequent untimely winter rains, higher incidence of root diseases (collar rot and wet root rot) due to high temperature and high soil moisture at early stage of crop growth, increased incidence of foliar diseases (botrytis gray mould, Ascochyta blight, Alternaria blight, stem rot etc.) due to excessive vegetative growth, and more aggression of weak pathogens causing dry root rot and collar rot are likely to cause huge damage to chickpea crop. Similarly, rise in atmospheric humidity at the time of flowering and podding stage may lead to higher activities of insect pests like gram pod borer, cut worm etc. Among various strategies to combat these challenges, strategies like screening of germplasm accessions to identify donors possessing traits of economic importance, diseases and insect pest resistance, tolerance to temperature extremities (cold and heat stress), frost, high or low soil moisture stress etc. will be of paramount importance. Careful screening of genetic resources (core or mini-core sets) including wild relatives and primitive landraces will become imperative. The mapping and tagging of gene(s) or quantitative trait loci (QTLs) responsible for imparting resistance/tolerance to abiotic and biotic stresses and yield attributes will be desirable for targeted transfer of the required traits. Further, rapid generation advancement and integration of molecular markers in enhancing efficiency of selection methods will ensure desired improvement in chickpea

Identification of a non-redundant set of 202 in silico SSR markers and applicability of a select set in chickpea (Cicer arietinum L.)

The paucity of sequence information flanking the simple sequence repeat (SSR) motifs identified especially in the transcript sequences has been limiting factor in the development of SSR markers for plant genome analysis as well as breeding applications. To overcome this and enhance the genic SSR marker repertoire in chickpea, the draft genome sequence of kabuli chickpea (CDC Frontier) and publicly available transcript sequences consisting of in silico identified SSR motifs were deployed in the present study. In this direction, the 300 bp sequence flanking the SSR motifs were retrieved by aligning 566 SSR containing transcripts of ICCV 2 available in public domain on the reference chickpea genome. A set of 202 novel genic SSRs were developed from a set of 507 primer pairs designed, based on in silico amplification of single locus and having no similarity to the publicly available SSR markers. Further, 40 genic SSRs equally distributed on chickpea genome were validated on a select set of 44 chickpea genotypes (including 41 Cicer arietinum and 3 Cicer reticulatum), out of which 25 were reported to be polymorphic. The polymorphism information content (PIC) value of 25 polymorphic genic SSRs ranged from 0.11 to 0.77 and number of alleles varied from 2 to 9. Clear demarcation among founder lines of multi-parent advanced generation inter-cross (MAGIC) population developed at ICRISAT and near-isogenic nature of JG 11 and JG11 + demonstrates the usefulness of these markers in chickpea diversity analysis and breeding studies. Further, genic polymorphic SSRs reported between parental lines of 16 different mapping populations along with the novel SSRs can be deployed for trait mapping and breeding applications in chickpea

Tapping the large genetic variability for salinity tolerance in chickpea

Salinity is an ever-increasing problem in agriculture worldwide and especially in Australia. Improved genotypes that are well adapted to saline conditions are needed to enhance and sustain production in these areas. A screening of 263 accessions of chickpea, including 211 accessions from ICRISAT’s mini-core collection (10% of the core collection and 1% of the entire collection), showed a six-fold range of variation for seed yield under salinity, with several genotypes yielding 20% more than the previously-released salinity tolerant cultivar CSG8962. No significant relation was found between biomass at the late vegetative stage and final seed yield under salinity. Performance of seed yield under salinity was explained in part by the yield potential under control conditions, and a salinity tolerance component. The major trait related to salinity tolerance was the ability to maintain under salinity a large number of viable pods with seeds. In contrast, the relative seed size under salinity did not differ between tolerant and sensitive genotypes. Preliminary analysis of genotypic data for approximately 50 SSR markers on 211 genotypes revealed some associations with salinity tolerance that deserve a detailed analysis. Future effort should focus on the effect of salinity on the reproductive stage of development

Whole genome re-sequencing reveals genome-wide variations among parental lines of 16 mapping populations in chickpea (Cicer arietinum L.)

Background Chickpea (Cicer arietinum L.) is the second most important grain legume cultivated by resource poor farmers in South Asia and Sub-Saharan Africa. In order to harness the untapped genetic potential available for chickpea improvement, we re-sequenced 35 chickpea genotypes representing parental lines of 16 mapping populations segregating for abiotic (drought, heat, salinity), biotic stresses (Fusarium wilt, Ascochyta blight, Botrytis grey mould, Helicoverpa armigera) and nutritionally important (protein content) traits using whole genome re-sequencing approach. Results A total of 192.19 Gb data, generated on 35 genotypes of chickpea, comprising 973.13 million reads, with an average sequencing depth of ~10 X for each line. On an average 92.18 % reads from each genotype were aligned to the chickpea reference genome with 82.17 % coverage. A total of 2,058,566 unique single nucleotide polymorphisms (SNPs) and 292,588 Indels were detected while comparing with the reference chickpea genome. Highest number of SNPs were identified on the Ca4 pseudomolecule. In addition, copy number variations (CNVs) such as gene deletions and duplications were identified across the chickpea parental genotypes, which were minimum in PI 489777 (1 gene deletion) and maximum in JG 74 (1,497). A total of 164,856 line specific variations (144,888 SNPs and 19,968 Indels) with the highest percentage were identified in coding regions in ICC 1496 (21 %) followed by ICCV 97105 (12 %). Of 539 miscellaneous variations, 339, 138 and 62 were inter-chromosomal variations (CTX), intra-chromosomal variations (ITX) and inversions (INV) respectively. Conclusion Genome-wide SNPs, Indels, CNVs, PAVs, and miscellaneous variations identified in different mapping populations are a valuable resource in genetic research and helpful in locating genes/genomic segments responsible for economically important traits. Further, the genome-wide variations identified in the present study can be used for developing high density SNP arrays for genetics and breeding applications

INTROGRESSION OF DROUGHT TOLERANCE ROOT TRAITS INTO KENYAN COMMERCIAL CHICKPEA VARIETIES USING MARKER ASSISTED BACKCROSSING

Roots play critical roles in enhancing drought tolerance, more so under terminal drought conditions. The objective of this study was to introgress drought tolerant root traits into Kenyan chickpea varieties through marker assisted backcrossing (MABC). Eight simple sequence repeat (SSR) markers, linked to quantitative trait loci (QTL) for root traits, were used to screen parents at ICRISAT in India, and 1144 single nucleotide polymorphic (SNPs) markers at Legume Genomics Centre in the United Kingdom. Crosses were made between two selected varieties, ICCV 92944 (Chania Desi II) and ICCV 00108 (LDT 068); and ICC 4958, QTL donor parent. Polymorphic SSR and SNP markers were used to select offspring with root QTL at F1, BC1F1, and BC2F1, and later advanced to BC2F3. BC2F3 families were evaluated for root traits at Egerton University in Kenya in a pot experiment under rain shelter. The BC2F3 families were significantly (P<0.05) different for root dry weight (RDW), shoot dry weight (SDW), total plant dry weight (PDW), and root to shoot dry weight (R/S) ratio (R/S) for Chania Desi II x ICC 4958; while R/S was significantly different for LDT 068 x ICC 4958. Root length density (RLD) and RDW were positively and significantly (P<0.05) correlated with most of the traits, indicating its usefulness in the indirect selection of these traits. The utilisation of MABC is an effective and efficient method of introgressing complex root traits into commercial lines, expected to improve yields under drought. There is need for deployment of marker-assisted breeding in difficult to phenotypically select traits.Les racines jouent un r\uf4le essentiel dans l\u2019am\ue9lioration de la tol\ue9rance \ue0 la s\ue9cheresse, plus encore en cas de s\ue9cheresse terminale. L\u2019objectif de cette \ue9tude \ue9tait d\u2019introduire des traits de racine tol\ue9rants \ue0 la s\ue9cheresse dans des vari\ue9t\ue9s Kenyannes de chickpea par r\ue9trocroisement assist\ue9 par marqueurs (MABC). Huit marqueurs de r\ue9p\ue9tition de s\ue9quence simple (SSR), li\ue9s \ue0 des locus de traits quantitatifs (QTL) pour les traits racinaires, ont \ue9t\ue9 utilis\ue9s pour s\ue9lectionner les parents \ue0 l\u2019ICRISAT en Inde, et 1144 marqueurs polymorphes \ue0 un seul nucl\ue9otide (SNP) au Legume Genomics Center au Royaume-Uni. Des croisements ont \ue9t\ue9 r\ue9alis\ue9s entre deux vari\ue9t\ue9s s\ue9lectionn\ue9es, ICCV 92944 (Chania Desi II) et ICCV 00108 (LDT 068) ; et ICC 4958, parent donneur QTL. Des marqueurs SSR et SNP polymorphes ont \ue9t\ue9 utilis\ue9s pour s\ue9lectionner la prog\ue9niture avec un QTL racine \ue0 F1, BC1F1 et BC2F1, puis avanc\ue9 \ue0 BC2F3. Les familles BC2F3 ont \ue9t\ue9 \ue9valu\ue9es pour les traits racinaires \ue0 l\u2019Universit\ue9 d\u2019Egerton au Kenya dans une exp\ue9rience en pot sous abri contre la pluie. Les familles BC2F3 \ue9taient significativement diff\ue9rentes (P<0,05) pour le poids sec des racines (RDW), le poids sec des pousses (SDW), le poids sec total de la plante (PDW) et le rapport poids sec des racines sur les pousses (R/S) (R/S ) pour Chania Desi II x ICC 4958\ua0; tandis que R/S \ue9tait significativement diff\ue9rent pour LDT 068 x ICC 4958. La densit\ue9 de longueur des racines (RLD) et RDW \ue9taient corr\ue9l\ue9es positivement et significativement (P < 0,05) avec la plupart des traits, indiquant son utilit\ue9 dans la s\ue9lection indirecte de ces traits. L\u2019utilisation de MABC est une m\ue9thode efficace et efficiente d\u2019introgression de traits racinaires complexes dans des lign\ue9es commerciales, cens\ue9e am\ue9liorer les rendements en p\ue9riode de s\ue9cheresse. Il est n\ue9cessaire de d\ue9ployer la s\ue9lection assist\ue9e par marqueurs dans les caract\ue8res difficiles \ue0 s\ue9lectionner ph\ue9notypiquement

Breeding Chickpea for Improved Adaptation to the Semi-Arid Tropical Environments

Chickpea (Cicer arietinum L.), also known as Garbanzo bean or Bengal gram, is the second most cultivated grain legume grown globally after dry bean (FAOSTAT data, 2007). It is cultivated annually on an area of about 10 million hectares over 50 countries. Over 80% of its area is in the semi-arid tropics (SAT) that encompass most of south Asia, parts of southeast Asia, a swathe across sub-Saharan Africa, much of southern and eastern Africa, and parts of Latin America. These regions are characterized by high atmospheric water demand, a high mean annual temperature, limited and erratic monsoonal rainfall, and nutrient poor soils. The major constraints to chickpea production in SAT include terminal drought and heat stresses, fusarium wilt and Helicoverpa pod borer. Soil salinity is also a major constraint to adaptation of chickpea in some areas, particularly in India, Pakistan, Bangladesh, Iran and Australia. High instances of dry root rot are reported from Sub- Saharan Africa and India. India is the largest chickpea producing country with 64% of global chickpea production (FAOSTAT data, 2007). Chickpea is grown on 6.7 m ha from latitude 32°N in northern India with cooler, long-season environment to 10°N in southern India with warmer, short season environment. There has been a large, shift in chickpea area from north to central and southern India, mainly because of expansion in area under irrigation and wheat cultivation in northern India. During the past four decades, chickpea area declined by about 4.2 m ha in northern and north-eastern states (Punjab, Haryana, Uttar Pradesh and Bihar) and increased by 2.6 m ha in central and southern states (Madhya Pradesh, Maharashtra, Karnataka and Andhra Pradesh). This drastic shift in chickpea cultivation from cooler, long-season environments to warmer, short-season environments resulted in chickpeas being more prone to abiotic and biotic stresses that are prevalent in warm short season environments (e.g. terminal drought and heat stresses). The crop improvement efforts at ICRISAT and National Agricultural Research System (NARS) in SAT countries have largely focused on improving adaptation of chickpea to SAT environments by enhancing resistance/tolerance to biotic and abiotic stresses prevalent in SAT environments. This paper reviews recent progress in breeding chickpea for improved adaptation to the SAT environments

Plant vigour QTLs co-map with an earlier reported QTL hotspot for drought tolerance while water saving QTLs map in other regions of the chickpea genome

Background Terminal drought stress leads to substantial annual yield losses in chickpea (Cicer arietinum L.). Adaptation to water limitation is a matter of matching water supply to water demand by the crop. Therefore, harnessing the genetics of traits contributing to plant water use, i.e. transpiration rate and canopy development dynamics, is important to design crop ideotypes suited to a varying range of water limited environments. With an aim of identifying genomic regions for plant vigour (growth and canopy size) and canopy conductance traits, 232 recombinant inbred lines derived from a cross between ICC 4958 and ICC 1882, were phenotyped at vegetative stage under well-watered conditions using a high throughput phenotyping platform (LeasyScan). Results Twenty one major quantitative trait loci (M-QTLs) were identified for plant vigour and canopy conductance traits using an ultra-high density bin map. Plant vigour traits had 13 M-QTLs on CaLG04, with favourable alleles from high vigour parent ICC 4958. Most of them co-mapped with a previously fine mapped major drought tolerance “QTL-hotspot” region on CaLG04. One M-QTL was found for canopy conductance on CaLG03 with the ultra-high density bin map. Comparative analysis of the QTLs found across different density genetic maps revealed that QTL size reduced considerably and % of phenotypic variation increased as marker density increased. Conclusion Earlier reported drought tolerance hotspot is a vigour locus. The fact that canopy conductance traits, i.e. the other important determinant of plant water use, mapped on CaLG03 provides an opportunity to manipulate these loci to tailor recombinants having low/high transpiration rate and plant vigour, fitted to specific drought stress scenarios in chickpea

Super Annigeri 1 and improved JG 74: Two Fusarium wilt-resistant introgression lines developed using marker-assisted backcrossing approach in chickpea (Cicer arietinum L.)

Annigeri 1 and JG 74 are elite high yielding desi cultivars of chickpea with medium maturity duration and extensively cultivated in Karnataka and Madhya Pradesh, respectively. Both cultivars, in recent years, have become susceptible to race 4 of Fusarium wilt (FW). To improve Annigeri 1 and JG 74, we introgressed a genomic region conferring resistance against FW race 4 (foc4) through marker-assisted backcrossing using WR 315 as the donor parent. For foreground selection, TA59, TA96, TR19 and TA27 markers were used at Agricultural Research Station, Kalaburagi, while GA16 and TA96 markers were used at Jawaharlal Nehru Krishi Vishwa Vidyalaya, Jabalpur. Background selection using simple sequence repreats (SSRs) for the cross Annigeri 1 × WR 315 in BC1F1 and BC2F1 lines resulted in 76–87% and 90–95% recurrent parent genome recovery, respectively. On the other hand, 90–97% genome was recovered in BC3F1 lines in the case of cross JG 74 × WR 315. Multilocation evaluation of 10 BC2F5 lines derived from Annigeri 1 provided one superior line referred to as Super Annigeri 1 with 8% increase in yield and enhanced disease resistance over Annigeri 1. JG 74315-14, the superior line in JG 74 background, had a yield advantage of 53.5% and 25.6% over the location trial means in Pantnagar and Durgapura locations, respectively, under Initial Varietal Trial of All India Coordinated Research Project on Chickpea. These lines with enhanced resistance and high yield performance are demonstration of successful deployment of molecular breeding to develop superior lines for FW resistance in chickpea