Identification of polymorphic SSR markers in elite genotypes of pearl millet and diversity analysis

Pearl millet is a climate-resilient crop of marginal agro-ecologies and semi-arid tropics of Asia and Africa. With substantial nutritional qualities crop requires low inputs and is capable of giving economic returns. Development of high-yielding hybrids is an important breeding objective for pearl millet worldwide. The knowledge of genetic diversity is a prerequisite for developing superior hybrids. In the current study, attempts were made to evaluate the diversity of 17 important Indian pearl millet inbred genotypes and one popular hybrid 9444 using fluorescent labeled SSR markers. A total of 342 polymorphic alleles with an average of 4.62 alleles per primer were produced from 74 SSR markers. Polymorphic information content (PIC) ranged from 0.10 to 0.89 with an average of 0.55. A very low level of heterozygosity was detected in genotypes. The average genetic dissimilarity detected between pairs of inbred lines was 0.66. Genetic dissimilarity estimates calculated among the inbred lines varied from 0.108 (AIMP-03 and AIMP-08) to a maximum of 0.851(AIMP-03/AIMP-08 and 81B). The results indicated that sufficient genetic variability is available in studied genotypes which can be exploited through heterosis breeding to develop hybrids. The study also presents a suit of SSR markers that could be effectively used for genetic diversity analysis in pearl millet

Discerning combining ability loci for divergent environments using chromosome segment substitution lines (CSSLs) in pearl millet

Pearl millet is an important crop for arid and semi-arid regions of the world. Genomic regions associated with combining ability for yield-related traits under irrigated and drought conditions are useful in heterosis breeding programs. Chromosome segment substitution lines (CSSLs) are excellent genetic resources for precise QTL mapping and identifying naturally occurring favorable alleles. In the present study, testcross hybrid populations of 85 CSSLs were evaluated for 15 grain and stover yield-related traits for summer and wet seasons under irrigated control (CN) and moisture stress (MS) conditions. General combining ability (GCA) and specific combining ability (SCA) effects of all these traits were estimated and significant marker loci linked to GCA and SCA of the traits were identified. Heritability of the traits ranged from 53–94% in CN and 63–94% in MS. A total of 40 significant GCA loci and 36 significant SCA loci were identified for 14 different traits. Five QTLs (flowering time, panicle number and panicle yield linked to Xpsmp716 on LG4, flowering time and grain number per panicle with Xpsmp2076 on LG4) simultaneously controlled both GCA and SCA, demonstrating their unique genetic basis and usefulness for hybrid breeding programs. This study for the first time demonstrated the potential of a set of CSSLs for trait mapping in pearl millet. The novel combining ability loci linked with GCA and SCA values of the traits identified in this study may be useful in pearl millet hybrid and population improvement programs using marker-assisted selection (MAS)

Construction of genetic linkage map and QTL analysis of sinksize traits in pearl millet (Pennisetum glaucum)

A linkage map, primarily based on SSCP-SNP markers, was constructed using 188 F2:3 (F2-derived F3) mapping population progenies derived from a cross between two pearl millet inbred lines having diverse pedigrees. The parents had large differences for two sink size traits (grain size and panicle diameter), and also differed for panicle length. The skeleton linkage map covered 1019 cM and it comprised of 44 loci (detected with 24 SSCP-SNP, 10 genomic SSR, 6 EST-SSR and 4 STS primer pairs) distributed across the seven linkage groups. Average adjacent-marker intervals ranged from 14 cM on LG1 to 38 cM on LG6, with an overall mean of 23 cM. Using the F2 linkage map and phenotypic data collected from the F2 and F2:3 generations of the mapping population, a total of 18 putative QTLs were detected for the three sink-size components. Eight QTLs explained 42.7% of observed phenotypic variation for panicle length, with individual QTLs explaining 6.1 to 18.2% using the F2:3 data set. For panicle diameter, 5 QTLs explained 45.8% of observed phenotypic variation with individual QTLs accounting for 6.3 to 30.2%. Similarly for grain size, 5 QTLs explained 29.6% of phenotypic variation with individual QTLs accounting for 6.1 to 8.9%. Genomic regions associated with panicle length, panicle diameter and grain size co-mapped on LG6 between Xpsms88 and Xpsms2270, indicating the existence of a gene or gene cluster with major effects involved in the control of significant proportions of the phenotypic variation for all three sink-size traits. The QTLs for panicle length on LG2 and LG6 (LOD>3 in both F2 and F2:3 data sets), for panicle diameter on LG2 and LG3 (LOD>14 in the F2:3 data set) and for grain size on LG3 and LG6 (LOD>3 in both F2 and F2:3 data sets) were identified as promising candidates for validation prior to possible application in marker-assisted breeding

Screening pearl millet germplasm for tolerance to soil salinity

Saline soils account for up to 580 million ha worldwide and are widespread In arid and semi-arid regions (Rengasamy 2002). Pearl millet [Pennisetum glaucum) is often grown In saline soils and Is known to be relatively better In tolerance to salinity than other crops, particularly maize (Zea mays) or legumes (Ashrafand McNeilly 1987, Dua 1989). However, a well-focused search can lead to the Identification of genotypes with superior tolerance. Since pearl millet Is usually grown rainfed with minimum Input, It Is all the more Important to genetically Improve the adaptation of this crop to soil salinity. The Improved salinity tolerant lines together with cultural management options provide greater scope for Improving the crop productivity in these saline soils

Applications of molecular markers in breeding

Molecular markers now provide appropriate complements to conventional breeding methods in most crops in ICRISAT’s germplasm conservation and crop improvement mandates. Where appropriate molecular markers are available, they are effective and sometimes appropriate, tools for crop improvement research addressing biological components in agricultural production systems. Molecular markers offer specific advantages in the assessment of genetic diversity and in trait-specific crop improvement. Molecular markers are almost infinitely superior to conventional morphological marker genes for mapping or tagging gene blocks associated with economically important traits. Gene tagging and QTL mapping in turn permit marker-assisted selection (MAS) in backcross, pedigree and population improvement programs, which can be especially useful for crop traits that are otherwise difficult or impossible to deal with by conventional means. Near-isogenic products of marker-assisted backcrossing programs can in turn provide not only improved cultivars, but also useful genetic tools facilitating improved understanding of mechanisms of abiotic stress tolerance or mechanisms of host plant resistance to pests and diseases that are critical components of integrated crop management systems. Finally, when relatively high-density marker-based fingerprinting of elite breeding lines is possible, this can be combined with pedigree information and multi-environment performance data sets to greatly enhance the ability of conventional breeding programs to design new cultivars, identify desirable recombinants, and track factors controlling complex traits and trait combinations

Assessment of opportunities to map pearl millet tolerance to salinity during germination and early seedling growth

Twenty-eight inbred lines of pearl millet (Pennisetum glaucum) obtained from ICRISAT, Patancheru, Andhra Pradesh, India, were evaluated for salt tolerance under laboratory conditions. Seeds were germinated on filter papers on Hoagland's solutions containing 0, 75, 100 or 150 mM NaCl. Fifteen seeds were germinated in each culture tube and the seedlings were allowed to grow for 10 days in the same nutrient solutions. The genotype × salinity interaction was significant for shoot and root lengths. Tift 23D2B1-P1-P5, ICMB 841-P3, P310-17-Bk, ICML 22 and ICMB 95333 were highly tolerant of salinity. Fifteen lines were moderately tolerant and 7 lines were sensitive. Large differences in germination salinity tolerance were detected between members of several pearl millet mapping population parental line pairs (including Tift 23D2B1 and WSIL-P8, ICMB 841-P3 and 863B-P2, and P310-17-Bk and W-504-1-P1 at 150 mM NaCl, and ICMP 451-P8 and 81B-P6, LGD 1-B-10 and ICMP 85417-P7, and PT 732B-P2 and P1449-2-P1 at 100 mM NaCl). Differences between mapping population parental line pairs were also detected for salinity tolerance of early seedling growth

Genetic diversity of stay-green sorghums and their derivatives revealed by microsatellites

The genetic variability of 28 sorghum genotypes of known senescence phenotype was investigated using 66 SSR markers well-distributed across the sorghum genome. The genotypes of a number of lines from breeding programmes for stay-green were also determined. This included lines selected phenotypically for stay-green and also RSG 03123, a marker-assisted backcross progeny of R16 (recurrent parent) and B35 (stay-green donor). A total of 419 alleles were detected with a mean of 6.2 per locus. The number of alleles ranged from one for Xtxp94 to 14 for Xtxp88. Chromosome SBI-10 had the highest mean number of alleles (8.33), while SBI-05 had the lowest (4.17). The PIC values obtained ranged from zero to 0.89 in Xtxp94 and Xtxp88, respectively, with a mean of 0.68. On a chromosome basis, mean PIC values were highest in SBI-10 (0.81) and lowest in SBI-05 (0.53). Most of the alleles from B35 in RSG 03123 were found on chromosomes SBI-01, SBI-02 and SBI-03, confirming the successful introgression of quantitative trait loci associated with stay-green from B35 into the senescent background R16. However, the alternative stay-green genetic sources were found to be distinct based on either all the SSRs employed or using only those associated with the stay-green trait in B35. Therefore, the physiological and biochemical basis of each stay-green source should be evaluated in order to enhance the understanding of the functioning of the trait in the various backgrounds. These genetic sources of stay-green could provide a valuable resource for improving this trait in sorghum breeding programmes

Identification of pearl millet [Pennisetum glaucum (L.) R.Br.] lines tolerant to soil salinity

Crop tolerance to salinity is of high importance due to the extent and the constant increase in salt-affected areas in arid and semi-arid regions. Pearl millet (Pennisetum glaucum), generally considered as fairly tolerant to salinity, could be an alternative crop option for salt affected areas. To explore the genotypic variability of vegetative-stage salinity tolerance, 100 pearl millet lines from ICRISAT breeding programs were first screened in a pot culture containing Alfisol with 250 mM NaCl solution as basal application. Subsequently, 31 lines including many parents of commercial hybrids, selected from the first trial were re-tested for confirmation of the initial salinity responses. Substantial variation for salinity tolerance was found on the basis of shoot biomass ratio (shoot biomass under salinity/ non-saline control) and 22 lines with a wide range of tolerance varying from highly tolerant to sensitive entries were identified. The performance of the genotypes was largely consistent across experiments. In a separate seed germination and seedling growth study, the seed germination was found to be adversely affected (more than 70% decrease) in more than half of the genotypes with 250 mM concentration of NaCl. The root growth ratio (root growth under salinity/control) as well as shoot growth ratio was measured at 6 DAS and this did not reflect the whole plant performance at 39 DAS. In general, the whole plant salinity tolerance was associated with reduced shoot N content, increased K+ and Na+ contents. The K+/Na+ and Ca++/Na+ ratios were also positively related to the tolerance but not as closely as the Na+ content. Therefore, it is concluded that a large scope exists for improving salt tolerance in pearl millet and that shoot Na+ concentration could be considered as a potential non-destructive selection criterion for vegetative-stage screening. The usefulness of this criterion for salinity response with respect to grain and stover yield remains to be investigated