Genetic variability, genotype × environment interaction and correlation analysis for grain iron and zinc contents in recombinant inbred line population of pearl millet [Pennisetum glaucum (L). R.

Micronutrient malnutrition is one of the major health problems, especially iron (Fe) and zinc (Zn) deficiencies that are widespread coupled with inadequate food supply in the developing world. Pearl millet grains are a good source of Fe and Zn elements making it a potential staple crop for overcoming hidden-hunger and micronutrient deficiencies. Breeding pearl millet with high levels of grain Zn and Fe contents represents a major opportunity to enhance the intake of these minerals for poor and malnourished people. A precise understanding of the genetic variability, correlation of mineral nutrients, genotype × environment (G × E) interaction is important for developing improved lines with high Fe and Zn content. To get fair estimates, we used a bi-parental recombinant inbred lines (RIL) mapping population representing F2 phenotypic variance. A total of 317 RILs were evaluated for grain iron and zinc content in two seasons, Summer 2016 (E1) and Summer 2017 (E2). The result from the analysis of variance exhibited a large variability for grain Fe and Zn content across the two environments. The G × E for high grain Fe were significant at P < 0.01. The mean performance across the two environments data for grain Fe ranged from 22.9 to 154.5 mg kg-1 (ppm) and Zn content ranged from 19.3 to 121 mg kg-1. The correlation coefficient for grain Fe and Zn was 0.9, and 0.8 and across the two (E1 and E2) environments. The value of correlation coefficient (0.9) was found to be highly significant at P < 0.01 level, that indicated good opportunities for simultaneous genetic improvement of both iron and zinc contents in pearl millet

Evaluation of global composite collection reveals agronomically superior germplasm accessions for chickpea improvement

The rich genetic diversity existing within exotic, indigenous, and diverse germplasm lays the foundation for the continuous improvement of crop cultivars. The composite collection has been suggested as a gateway to identifying superior germplasm for use in crop improvement programs. Here, a chickpea global composite collection was evaluated at five locations in India over two years for five agronomic traits to identify agronomically superior accessions. The desi, kabuli, and intermediate types of chickpea accessions differed significantly for plant height (PLHT) and 100-seed weight (100 SW). In contrast, the intermediate type differed substantially from kabuli for days to maturity (DM). Several highly significant trait correlations were detected across different locations. The most stable and promising accessions from each of the five locations were prioritised based on their superior performance over the best-performing check cultivar. Accordingly, the selected germplasm accessions of desi type showed up to 176% higher seed yield (SY), 29% lower flowering time, 21% fewer maturity days, 64% increase in PLHT, and 183% larger seeds than the check cultivar JG11 or Annigeri. The prioritised kabuli accessions displayed up to 270% more yield, 13% less flowering time, 8% fewer maturity days, 111% increase in PLHT, and 41% larger seeds over the check cultivar KAK2. While the intermediate type accessions had up to 169% better yield, 1% early flowering, 3% early maturity, 54% taller plants, and 25% bigger seeds over the check cultivar JG 11 or KAK2. These accessions can be utilised in chickpea improvement programs to develop high-yielding, early flowering, short duration, taller, and large-seeded varieties with a broad genetic base

Double-digest restriction-associated DNA sequencing-based genotyping and its applications in sesame germplasm management

Sesame (Sesamum indicum L.) is an ancient oilseed crop belonging to the family Pedaliaceae and a globally cultivated crop for its use as oil and food. In this study, 2496 sesame accessions, being conserved at the National Genebank of ICAR-National Bureau of Plant Genetic Resources (NBPGR), were genotyped using genomics-assisted double-digest restriction-associated DNA sequencing (ddRAD-seq) approach. A total of 64,910 filtered single-nucleotide polymorphisms (SNPs) were utilized to assess the genome-scale diversity. Applications of this genome-scale information (reduced representation using restriction enzymes) are demonstrated through the development of a molecular core collection (CC) representing maximal SNP diversity. This information is also applied in developing a mid-density panel (MDP) comprising 2515 hyper-variable SNPs, representing almost equally the genic and non-genic regions. The sesame CC comprising 384 accessions, a representative set of accessions with maximal diversity, was identified using multiple criteria such as k-mer (subsequence of length “k” in a sequence read) diversity, observed heterozygosity, CoreHunter3, GenoCore, and genetic differentiation. The coreset constituted around 15% of the total accessions studied, and this small subset had captured >60% SNP diversity of the entire population. In the coreset, the admixture analysis shows reduced genetic complexity, increased nucleotide diversity (π), and is geographically distributed without any repetitiveness in the CC germplasm. Within the CC, India-originated accessions exhibit higher diversity (as expected based on the center of diversity concept), than those accessions that were procured from various other countries. The identified CC set and the MDP will be a valuable resource for genomics-assisted accelerated sesame improvement program

Assessment of nodulation potential in mini-core genotypes and land races of chickpea

Symbiotic nitrogen fixation (SNF) is a sustainable alternative for nitrogen supply for plants in agriculture. Past efforts to enhance SNF in chickpea through inoculation with improved rhizobia were partially successful. Hence, there is an urgent need to identify nodulation variants among the mini-core and races accessions of chickpea. In the present study, a total of 211 mini-core lines, 68 land races and 3 checks were evaluated for nodulation variants under greenhouse conditions at ICRISAT, Patancheru, India and IIPR, Kanpur, India. The seeds of all accessions were inoculated with IC-76, a nodulating bacteria, on both locations. When the potting material was pasteurized, the organic carbon had reduced from 0.49% to 0.29% whereas no significant difference was noted in total N and available P contents. At 45 days after sowing, the mini-core lines of chickpea were categorized into 6 types, based on nodulation capability (rating 0-5, where 0=no nodules; while 5 = maximum nodules) at both ICRISAT and IIPR locations. A direct correlation was obtained between nodule numbers and shoot and root weights. Further, some lines were found common at both the locations for particular category of nodulation rating.For instance, the lines ICC-2580, ICC- 2990, ICC-3421 and RSG-888 were found fitting in rating 5 while lines ICC-6294 and ICC-9002 in rating 1. A similar trend of nodulation variants were also found in the land races of chickpea. A total of 35 chickpea mini-core lines and six land races were found common for nodulation variants at both locations

Genetic analysis of resistance to post flowering stalk rot in tropical germplasm of maize ( Zea mays L.)

Post flowering stalk rot (PFSR) is one of the major biotic constraints to maize production in tropical and sub-tropical environments. It is a complex disease caused by multiple pathogens, among which Fusarium moniliforme and Macrophomina phaseolina are the major ones that cause severe yield losses in the Asian tropics. A set of maize inbred lines was evaluated at two locations for Fusarium stalk rot (FSR) and Macrophomina stalk rot (MSR). Based on line evaluation trials, resistant and susceptible lines were selected and crossed following a Diallel mating design IV to study the gene action for resistance to these stalk rots and the estimating the combining ability of inbred lines. A 9 × 9 diallel (Diallel-A) produced 36 hybrids for studying FSR resistance, and a 12 × 12 diallel (Diallel-B) produced 66 hybrids to analyse the resistance towards both FSR and MSR. These hybrids were evaluated at two locations for MSR and one location for FSR with artificial inoculation. The hybrids differed significantly for FSR (p < 0.05), as was the general combining ability (GCA) effects (p < 0.01), while Specific combining ability (SCA) effects were found to be non-significant. The analysis of the trials under MSR, showed significant difference for GCA, SCA, GCA × environment (p < 0.01), and hybrid × environment (p < 0.05) while SCA × environment was non-significant. The Baker ratio, which shows the relative importance of GCA over SCA, was close to unity for both the stalk rots, and hence a predominant additive gene effect was inferred towards resistance to these diseases. Though the GCA × environment interaction was significant for MSR, this study identified lines and their cross combinations with high resistance and large GCA and SCA effects across environments for FSR and MSR This offers scope for source population improvement for resistance to these stalk rots, as well as developing maize hybrids with stable resistance to Post flowering stalk rot

Genome-Wide DArTSeq Genotyping and Phenotypic Based Assessment of Within and Among Accessions Diversity and Effective Sample Size in the Diverse Sorghum, Pearl Millet, and Pigeonpea Landraces

Germplasm should be conserved in such a way that the genetic integrity of a given accession is maintained. In most genebanks, landraces constitute a major portion of collections, wherein the extent of genetic diversity within and among landraces of crops vary depending on the extent of outcrossing and selection intensity infused by farmers. In this study, we assessed the level of diversity within and among 108 diverse landraces and wild accessions using both phenotypic and genotypic characterization. This included 36 accessions in each of sorghum, pearl millet, and pigeonpea, conserved at ICRISAT genebank. We genotyped about 15 to 25 individuals within each accession, totaling 1,980 individuals using the DArTSeq approach. This resulted in 45,249, 19,052, and 8,211 high-quality single nucleotide polymorphisms (SNPs) in pearl millet, sorghum, and pigeonpea, respectively. Sorghum had the lowest average phenotypic (0.090) and genotypic (0.135) within accession distances, while pearl millet had the highest average phenotypic (0.227) and genotypic (0.245) distances. Pigeonpea had an average of 0.203 phenotypic and 0.168 genotypic within accession distances. Analysis of molecular variance also confirms the lowest variability within accessions of sorghum (26.3%) and the highest of 80.2% in pearl millet, while an intermediate in pigeonpea (57.0%). The effective sample size required to capture maximum variability and to retain rare alleles while regeneration ranged from 47 to 101 for sorghum, 155 to 203 for pearl millet, and 77 to 89 for pigeonpea accessions. This study will support genebank curators, in understanding the dynamics of population within and among accessions, in devising appropriate germplasm conservation strategies, and aid in their utilization for crop improvement

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

Plant growth-promoting traits of biocontrol potential bacteria isolated from rice rhizosphere

Seven isolates of bacteria (SRI-156, SRI-158, SRI-178, SRI-211, SRI-229, SRI-305 and SRI-360) were earlier reported by us as having potential for biocontrol of charcoal rot of sorghum and plant growth promotion (PGP) of the plant. In the present study, the seven isolates were characterized for their physiological traits (tolerance to salinity, pH, temperature and resistance to antibiotics and fungicides) and further evaluated in the field for their PGP of rice. All the seven isolates were able to grow at pH values between 5 and 13, in NaCl concentrations of up to 8% (except SRI-156 and SRI-360), temperatures between 20 and 40?C and were resistant to ampicillin (>100 ppm; except SRI-158 and SRI-178) but sensitive (<10 ppm) to chloramphenicol, kanamycin, nalidixic acid, streptomycin (except SRI-156 and SRI-211) and tetracycline. They were tolerant to fungicides benlate and captan, except SRI-158 and SRI-178, bavistin and sensitive to thiram (except SRI-156 and SRI-211) at field application level. In the field, four of the seven isolates (SRI-158, SRI-211, SRI-229 and SRI-360) significantly enhanced the tiller numbers, stover and grain yields, total dry matter, root length, volume and dry weight over the un-inoculated control. In the rhizosphere soil at harvest, all the isolates significantly enhanced microbial biomass carbon (except SRI-156), microbial biomass nitrogen and dehydrogenase activity (up to 33%, 36% and 39%, respectively) and total N, available P and% organic carbon (up to 10%, 38% and 10%, respectively) compared to the control. This investigation further confirms that the SRI isolates have PGP properties

Genomic-enabled prediction model with genotype × environment interaction in elite chickpea lines

Genomic selection (GS) allows safe phenotyping and reduces cost and shortening selection cycles. Incorporating of genotype × environment (G×E) interactions in genomic prediction models improves the predictive ability of lines performance across environments and in target environments. Phenotyping data on a set of 320 elite chickpea breeding lines on different traits (e.g., plant height, days to maturity, and seed yield), from three consecutive years for two different treatments at two locations were recorded. These lines were genotyped on DArTseq(1.6K) and Genotyping- by-Sequencing (GBS; 89K SNPs) platforms. Five different models were fitted, four of which included genomic information as main effects (baseline model) and/or G×E interactions. Three different cross-validation schemes that mimic real scenarios that breeders might face on fields were considered to assess the predictive ability of the models (CV2: incomplete field trials; CV1: newly developed lines; and CV0: new previously untested environments). Different prediction models gave different results for the different traits; however, some interesting patterns were observed. For CV1, analyzing yield seed interaction models improved baseline counterparts on an average between 55 and 92% using DArT and DArT combined with GBS data, respectively [between 9 and 112% for all traits]. While for CV2 these improvements varied b tween 65 and 102% [between 8 and 130% remaining traits]. In CV0, no clear advantage was observed considering the interaction term. These results suggest that GS models hold potential for breeder’s applications on chickpea cultivar improvements

Phylogenetic diversity of Mesorhizobium in chickpea

Crop domestication, in general, has reduced genetic diversity in cultivated gene pool of chickpea (Cicer arietinum) as compared with wild species (C. reticulatum, C. bijugum). To explore impact of domestication on symbiosis, 10 accessions of chickpeas, including 4 accessions of C. arietinum, and 3 accessions of each of C. reticulatum and C. bijugum species, were selected and DNAs were extracted from their nodules. To distinguish chickpea symbiont, preliminary sequences analysis was attempted with 9 genes (16S rRNA, atpD, dnaJ, glnA, gyrB, nifH, nifK, nodD and recA) of which 3 genes (gyrB, nifK and nodD) were selected based on sufficient sequence diversity for further phylogenetic analysis. Phylogenetic analysis and sequence diversity for 3 genes demonstrated that sequences from C. reticulatum were more diverse. Nodule occupancy by dominant symbiont also indicated that C. reticulatum (60%) could have more various symbionts than cultivated chickpea (80%). The study demonstrated that wild chickpeas (C. reticulatum) could be used for selecting more diverse symbionts in the field conditions and it implies that chickpea domestication affected symbiosis negatively in addition to reducing genetic diversity