Use of Genomic Estimated Breeding Values Results in Rapid Genetic Gains for Drought Tolerance in Maize.

More than 80% of the 19 million ha of maize ( L.) in tropical Asia is rainfed and prone to drought. The breeding methods for improving drought tolerance (DT), including genomic selection (GS), are geared to increase the frequency of favorable alleles. Two biparental populations (CIMMYT-Asia Population 1 [CAP1] and CAP2) were generated by crossing elite Asian-adapted yellow inbreds (CML470 and VL1012767) with an African white drought-tolerant line, CML444. Marker effects of polymorphic single-nucleotide polymorphisms (SNPs) were determined from testcross (TC) performance of F families under drought and optimal conditions. Cycle 1 (C1) was formed by recombining the top 10% of the F families based on TC data. Subsequently, (i) C2[PerSe_PS] was derived by recombining those C1 plants that exhibited superior per se phenotypes (phenotype-only selection), and (ii) C2[TC-GS] was derived by recombining a second set of C1 plants with high genomic estimated breeding values (GEBVs) derived from TC phenotypes of F families (marker-only selection). All the generations and their top crosses to testers were evaluated under drought and optimal conditions. Per se grain yields (GYs) of C2[PerSe_PS] and that of C2[TC-GS] were 23 to 39 and 31 to 53% better, respectively, than that of the corresponding F population. The C2[TC-GS] populations showed superiority of 10 to 20% over C2[PerSe-PS] of respective populations. Top crosses of C2[TC-GS] showed 4 to 43% superiority of GY over that of C2[PerSe_PS] of respective populations. Thus, GEBV-enabled selection of superior phenotypes (without the target stress) resulted in rapid genetic gains for DT.

Genomic Regions Associated with Root Traits under Drought Stress in Tropical Maize (Zea mays L.).

An association mapping panel, named as CIMMYT Asia association mapping (CAAM) panel, involving 396 diverse tropical maize lines were phenotyped for various structural and functional traits of roots under drought and well-watered conditions. The experiment was conducted during Kharif (summer-rainy) season of 2012 and 2013 in root phenotyping facility at CIMMYT-Hyderabad, India. The CAAM panel was genotyped to generate 955, 690 SNPs through GBS v2.7 using Illumina Hi-seq 2000/2500 at Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA. GWAS analysis was carried out using 331,390 SNPs filtered from the entire set of SNPs revealed a total of 50 and 67 SNPs significantly associated for root functional (transpiration efficiency, flowering period water use) and structural traits (rooting depth, root dry weight, root length, root volume, root surface area and root length density), respectively. In addition to this, 37 SNPs were identified for grain yield and shoot biomass under well-watered and drought stress. Though many SNPs were found to have significant association with the traits under study, SNPs that were common for more than one trait were discussed in detail. A total 18 SNPs were found to have common association with more than one trait, out of which 12 SNPs were found within or near the various gene functional regions. In this study we attempted to identify the trait specific maize lines based on the presence of favorable alleles for the SNPs associated with multiple traits. Two SNPs S3_128533512 and S7_151238865 were associated with transpiration efficiency, shoot biomass and grain yield under well-watered condition. Based on favorable allele for these SNPs seven inbred lines were identified. Similarly, four lines were identified for transpiration efficiency and shoot biomass under drought stress based on the presence of favorable allele for the common SNPs S1_211520521, S2_20017716, S3_57210184 and S7_130878458 and three lines were identified for flowering period water-use, transpiration efficiency, root dry weight and root volume based on the presence of favorable allele for the common SNPs S3_162065732 and S3_225760139.

Genetic diversity analysis in valencia peanut (Arachis hypogaea L.) using microsatellite markers.

Cultivated peanut or groundnut (Arachis hypogaea L) is an important source of oil and protein. Considerable variation has been recorded for morphological, physiological and agronomic traits, whereas few molecular variations have been recorded for this crop. The identification and understanding of molecular genetic diversity in cultivated peanut types will help in effective genetic conservation along with efficient breeding programs in this crop. The New Mexico breeding program has embarked upon a program of improvement of Valencia peanut (belonging to the sub species fastigiata), because efforts to improve the yield potential are lacking due to lack of identified divergent exotic types. For the first time, this study has shown molecular diversity using microsatellite markers in the cultivated Valencia peanut (sub spp. fastigiata) from around the globe. In this investigation, 48 cultivated Valencia peanut genotypes have been selected and analyzed using 18 fluorescently labeled SSR (f-SSR) primer pairs. These primer pairs amplified 120 polymorphic loci among the genotypes screened and amplified from 3 to 19 alleles with an average of 6.9 allele per primer pair. The f-SSR marker data was further analyzed using cluster algorithms and principal component analysis. The results indicated that (1) considerable genetic variations were discovered among the analyzed genotypes; (2) The f-SSR based clustering could identify the putative pedigree types of the present Valencia types of diverse origins, and (3) The f-SSR in general is sufficient to obtain estimates of genetic divergence for the material in study. The results are being utilized in our breeding program for parental selection and linkage map construction.