Designed and validated novel allele-specific primer to differentiate Kernel Row Number (KRN) in tropical field corn.

BACKGROUND: Kernel row number (KRN) is an important yield component trait with a direct impact on the productivity of maize. The variability in KRN is influenced by the inflorescence meristem size, which is determined by the CLAVATA-WUSCHEL pathway. A CLAVATA receptor-like protein, encoded by the FASCIATED EAR2 (fea2gene), enhances the growth of inflorescence meristem and is thus involved in the determination of KRN. The amplicon sequencing-based method was employed to dissect the allelic variation of the fea2 gene in tropical field corn. METHODOLOGY/PRINCIPAL FINDING: Amplicon-based sequencing of AI 535 (Low KRN) and AI 536 (High KRN) was undertaken for the gene fea 2 gene that codes for KRN in maize. Upon multiple sequence alignment of both sequences, A to T transversion at the 1311 position was noticed between Low KRN and High KRN genotypes resulting in different allelic forms of a fea2 gene in tropical maize. An allele-specific primer 1311 fea2.1 was designed and validated that can differentiate High and Low KRN genotypes. CONCLUSION/SIGNIFICANCE: Maize has high variability for KRN and is exemplified by the wide values ranging from 8-26 KRN in the maize germpalsm. The sequence-based approach of SNP detection through the use of a specific primer facilitated the detection of variation present in the target trait. This makes it possible to capture these variations in the early generation. In the study, the PCR-based differentiation method described for the identification of desirable high KRN genotypes would augment the breeding programs for improving the productivity of field corn.

Timely sown maize hybrids improve the post-anthesis dry matter accumulation, nutrient acquisition and crop productivity.

Delayed sowing of maize hybrids could exacerbate the capability of maximizing the yield potential through poor crop stand, root proliferation, nutrient uptake, and dry matter accumulation coupled with the inadequate partitioning of the assimilates. This study appraised the performance of five recent maize hybrids viz., PMH-1, PJHM-1, AH-4158, AH-4271, and AH-8181 under timely and late sown conditions of the irrigated semi-arid ecologies. Timely sowing had the grain and stover yields advantage of 16-19% and 12-25%, respectively over the late sown maize hybrids. The advanced hybrids AH-4271 and AH-4158 had higher grain yields than the others. During the post-anthesis period, a greater dry matter accumulation and contribution to the grain yield to the tune of 16% and 10.2%, respectively, was observed under timely sown conditions. Furthermore, the nutrient acquisition and use efficiencies also improved under the timely sown. The nutrient and dry matter remobilization varied among the hybrids with AH-4271 and PMH-1 registering greater values. The grain yield stability index (0.85) was highest with AH-4158 apart from the least yield reduction (15.2%) and stress susceptibility index (0.81), while the maximum geometric mean productivity was recorded with the AH-4271 (5.46 Mg ha-1). The hybrids AH-4271 and PJHM-1 exhibited improved root morphological traits, such as root length, biomass, root length density, root volume at the V5 stage (20 days after sowing, DAS) and 50% flowering (53 DAS). It is thus evident that the timely sowing and appropriate hybrids based on stress tolerance indices resulted in greater yields and better utilization of resources.

Genetic variability, combining ability and molecular diversity-based parental line selection for heterosis breeding in field corn (Zea mays L.).

BACKGROUND: The demand of maize crop is increasing day by day, hence to reduce the production and demand gap, there is a need to extract the high yielding parental lines to improve per se yield of the hybrids, which could help to enhance the productivity in maize crops. METHODS AND RESULTS: The present investigation was carried out to select the best medium maturing inbred lines, among a set of 118 inbred lines. Based on the Duncan multiple range test, out of 118 lines, 16 inbred lines were selected on the basis of its high yield per se and flowering time. The molecular diversity was carried out using SSR markers linked to heterotic QTL and up on diversity analysis it classified selected genotypes in to three distinct groups. Among the selected inbred lines, a wider genetic variability and molecular diversity were observed. A total of 39 test crosses were generated after classifying 16 inbred lines in to three testers and thirteen lines (based on per se grain yield and molecular diversity) and crossing them in line × tester manner. CONCLUSION: Combining ability analysis of these parental lines showed that female parents, PML 109, PML 110, PML 111, PML 114 and PML 116 showed additive effect for KRN and grain yield, whereas male parents, PML 46, and PML 93 showed epistatic effect for KRN and PML 102 showed epistatic effect for grain yield. The generated information in the present investigation may be exploited for heterosis breeding in filed corn. KEY MESSAGES: To tackle the balanced dietary requirement of Indian population; we focused to enhance the productivity of maize hybrids using genetically broad based, elite, diverse inbred lines. Combination of selection criterion, not only augment the productivity but also improves the quality of hybrid/s.

Conservation agriculture based integrated crop management sustains productivity and economic profitability along with soil properties of the maize-wheat rotation.

Field experiments were conducted to evaluate eight different integrated crop management (ICM) modules for 5 years in a maize-wheat rotation (MWR); wherein, ICM1&2-'business-as-usual' (conventional flatbed maize and wheat, ICM3&4-conventional raised bed (CTRB) maize and wheat without residues, ICM5&6-conservation agriculture (CA)-based zero-till (ZT) flatbed maize and wheat with the residues, and ICM7&8- CA-based ZT raised bed maize and wheat with the residues. Results indicated that the ICM7&8 produced significantly (p < 0.05) the highest maize grain yield (5 years av.) which was 7.8-21.3% greater than the ICM1-6. However, across years, the ICM5-8 gave a statistically similar wheat grain yield and was 8.4-11.5% greater than the ICM1-4. Similarly, the CA-based residue retained ICM5-8 modules had given 9.5-14.3% (5 years av.) greater system yields in terms of maize grain equivalents (MGEY) over the residue removed CT-based ICM1&4. System water productivity (SWP) was the highest with ICM5-8, being 10.3-17.8% higher than the ICM1-4. Nevertheless, the highest water use (TWU) was recorded in the CT flatbed (ICM1&2), ~ 7% more than the raised bed and ZT planted crops with or without the residues (ICM4-8). Furthermore, the ICM1-4 had produced 9.54% greater variable production costs compared to the ICM5-8, whereas, the ICM5-8 gave 24.3-27.4% additional returns than the ICM1-4. Also, different ICM modules caused significant (p < 0.05) impacts on the soil properties, such as organic carbon (SOC), microbial biomass carbon (SMBC), dehydrogenase (SDH), alkaline phosphatase (SAP), and urease (URE) activities. In 0.0-0.15 m soil profile, residue retained CA-based (ICM5-8) modules registered a 7.1-14.3% greater SOC and 10.2-17.3% SMBC than the ICM1-4. The sustainable yield index (SYI) of MWR was 13.4-18.6% greater under the ICM7&8 compared to the ICM1-4. Hence, this study concludes that the adoption of the CA-based residue retained ICMs in the MWR could sustain the crop yields, enhance farm profits, save water and improve soil properties of the north-western plans of India.

Genomics-Enabled Next-Generation Breeding Approaches for Developing System-Specific Drought Tolerant Hybrids in Maize.

Breeding science has immensely contributed to the global food security. Several varieties and hybrids in different food crops including maize have been released through conventional breeding. The ever growing population, decreasing agricultural land, lowering water table, changing climate, and other variables pose tremendous challenge to the researchers to improve the production and productivity of food crops. Drought is one of the major problems to sustain and improve the productivity of food crops including maize in tropical and subtropical production systems. With advent of novel genomics and breeding tools, the way of doing breeding has been tremendously changed in the last two decades. Drought tolerance is a combination of several component traits with a quantitative mode of inheritance. Rapid DNA and RNA sequencing tools and high-throughput SNP genotyping techniques, trait mapping, functional characterization, genomic selection, rapid generation advancement, and other tools are now available to understand the genetics of drought tolerance and to accelerate the breeding cycle. Informatics play complementary role by managing the big-data generated from the large-scale genomics and breeding experiments. Genome editing is the latest technique to alter specific genes to improve the trait expression. Integration of novel genomics, next-generation breeding, and informatics tools will accelerate the stress breeding process and increase the genetic gain under different production systems.

Biochemical and molecular dissection of thermo-sensitive genetic male sterility in diploid cotton (Gossypium arboreum L).

Diploid cotton, due to its inherent problem of stamen brittleness, its found unsuitable for traditional method of hybrid seed production which involves hand emasculation followed by pollination. Due to shortfall in other methods viz., Genetic Male Sterility (GMS), as well as, Cytoplasmic Genetic Male Sterility (CGMS), hybrid seed production in diploid cotton becomes costly and thereby, covers less area among the total cotton grown area. Thermo-sensitive genetic male sterility, which overcomes the drawbacks of both GMS and CGMS can be an effective tool in coming years for hybrid cotton research. Understanding fertility and sterility variations, their relation with biochemical changes in plant is important before its application in plant breeding. Hence, the available TGMS line, Ga TGMS-3 obtained at Cotton Research Centre, UAS, Dharwad was studied for callase activity and markers associated with TGMS. The line Ga TGMS-3 had fertile anthers and showed less callase enzyme activity at pre-meiosis stage, high enzyme activity at tetrad releasing microspore stage and no callase activity during other stages. The counterpart TGMS sterile anthers displayed little higher callase activity at pre-meiosis stage, high activity at tetrad stage, but poor activity at tetrad releasing microspore stage. During tetrad stage, TGMS sterile anthers showed high callase enzyme activity giving every chance for early release of poorly developed microspores as compared to fertile anthers. At tetrad releasing microspores stage during which fertile anthers had strong callase enzyme activity led to microspores being released normally and developed normal pollen grains as compared to sterile anthers. The present investigation revealed that NAU2176, NAU2096 and BNL1227 primers can be used as tightly linked markers for TGMS trait, as evident from their differential expression in fertile and sterile anthers.

Genomewide association studies for 50 agronomic traits in peanut using the 'reference set' comprising 300 genotypes from 48 countries of the semi-arid tropics of the world.

Peanut is an important and nutritious agricultural commodity and a livelihood of many small-holder farmers in the semi-arid tropics (SAT) of world which are facing serious production threats. Integration of genomics tools with on-going genetic improvement approaches is expected to facilitate accelerated development of improved cultivars. Therefore, high-resolution genotyping and multiple season phenotyping data for 50 important agronomic, disease and quality traits were generated on the 'reference set' of peanut. This study reports comprehensive analyses of allelic diversity, population structure, linkage disequilibrium (LD) decay and marker-trait association (MTA) in peanut. Distinctness of all the genotypes can be established by using either an unique allele detected by a single SSR or a combination of unique alleles by two or more than two SSR markers. As expected, DArT features (2.0 alleles/locus, 0.125 PIC) showed lower allele frequency and polymorphic information content (PIC) than SSRs (22.21 alleles /locus, 0.715 PIC). Both marker types clearly differentiated the genotypes of diploids from tetraploids. Multi-allelic SSRs identified three sub-groups (K = 3) while the LD simulation trend line based on squared-allele frequency correlations (r2) predicted LD decay of 15-20 cM in peanut genome. Detailed analysis identified a total of 524 highly significant MTAs (p value > 2.1 × 10-6) with wide phenotypic variance (PV) range (5.81-90.09%) for 36 traits. These MTAs after validation may be deployed in improving biotic resistance, oil/ seed/ nutritional quality, drought tolerance related traits, and yield/ yield components.